@prefix LoadListingRequirement: <http://commonwl.org/cwltool#LoadListingRequirement/> .
@prefix SchemaDefRequirement: <https://w3id.org/cwl/cwl#SchemaDefRequirement/> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix sld:   <https://w3id.org/cwl/salad#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .
@prefix NetworkAccess: <http://commonwl.org/cwltool#NetworkAccess/> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix ScatterMethod: <https://w3id.org/cwl/cwl#ScatterMethod/> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .
@prefix ResourceRequirement: <https://w3id.org/cwl/cwl#ResourceRequirement/> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/bait_intervals> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/normal_target_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/intervals_target> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/intervals_antitarget> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/reference_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/tumor_bin_level_ratios> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/normal_antitarget_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/tumor_antitarget_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/cn_scatter_plot> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/tumor_segmented_ratios> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/tumor_target_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/cn_diagram> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/annotate_coding_only>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#annotate_coding_only> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_bams_samtools.cwl#bams>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "vcf index" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/tabix" "-p" "vcf"
                                 ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl#indexed_vcf> ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_summary_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/summary_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/custom_gnomad_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#custom_gnomad_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#vep_summary>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "annotated.vcf_summary.html" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf/sample_name>
        cwl:default  "NORMAL" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#picard_metric_accumulation_level>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/mutect_max_alt_alleles_in_normal_count>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_max_alt_alleles_in_normal_count> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_target_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/apply_bqsr.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_target_coverage>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/normal_target_coverage> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#min_coverage>
        cwl:default       8 ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/annotate_coding_only>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#annotate_coding_only> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Unaligned to aligned BAM" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#align_and_tag> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#readgroup> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#tagged_bam> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id_depth>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id/verify_bam_id_depth> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#region_filter/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#exome_mode>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_snvs/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/summary_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_base_intervals> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_target_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/summary_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_base_coverage_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_min_coverage>
        cwl:default  8 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/remove_end_tags.cwl#processed_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "pindel.noend.vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/roi_bed>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#intervals_to_bed/interval_bed> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#summary_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/summary_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic_hc_indels>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/somatic_hc> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/output_prefix>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_base_intervals> ;
        cwl:valueFrom  "base-$(self.label)" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_ensembl_species>
        rdfs:comment  "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_per_base_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_base_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#bam_readcount_tsv>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/cosmic_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cosmic_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mark_duplicates_and_sort.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Mark duplicates and Sort" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(runtime.cores)"
                                   ]
                                   [ CommandLineBinding:position  4 ;
                                     cwl:valueFrom                "$(inputs.bam.nameroot).mark_dups_metrics.txt"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(runtime.cores)"
                                   ]
                                   [ CommandLineBinding:position  4 ;
                                     cwl:valueFrom                "$(inputs.bam.nameroot).mark_dups_metrics.txt"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "/bin/bash" "markduplicates_helper.sh" ) ;
        cwl:baseCommand          ( "/bin/bash" "markduplicates_helper.sh" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mark_duplicates_and_sort.cwl#input_sort_order> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mark_duplicates_and_sort.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mark_duplicates_and_sort.cwl#output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mark_duplicates_and_sort.cwl#metrics_file> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mark_duplicates_and_sort.cwl#sorted_bam> ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "set -o pipefail\nset -o errexit\n\ndeclare MD_BARCODE_TAG\nif [ ! -z \"$6\" ]; then\n  MD_BARCODE_TAG=\"BARCODE_TAG=$6\"\n/usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT \"$MD_BARCODE_TAG\" | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nelse\n  /usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nfi\n" ;
                                                  cwl:entryname  "markduplicates_helper.sh"
                                                ]
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  [ cwl:entry      "set -o pipefail\nset -o errexit\n\ndeclare MD_BARCODE_TAG\nif [ ! -z \"$6\" ]; then\n  MD_BARCODE_TAG=\"BARCODE_TAG=$6\"\n/usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT \"$MD_BARCODE_TAG\" | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nelse\n  /usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nfi\n" ;
                                                  cwl:entryname  "markduplicates_helper.sh"
                                                ]
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/mark_duplicates-cwl:1.0.1"
                                 ] ;
        cwl:requirements         [ a                             cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin  8 ;
                                   ResourceRequirement:ramMin    40000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/mark_duplicates-cwl:1.0.1"
                                 ] ;
        cwl:requirements         [ a                             cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin  8 ;
                                   ResourceRequirement:ramMin    40000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "varscan v2.4.2 processSomatic" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "cp" "$(inputs.variants.path)" "$(runtime.outdir)/$(inputs.variants.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "java" "-jar" "/opt/varscan/VarScan.jar" "processSomatic"
                                 ) ;
        cwl:arguments            ( "cp" "$(inputs.variants.path)" "$(runtime.outdir)/$(inputs.variants.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "java" "-jar" "/opt/varscan/VarScan.jar" "processSomatic"
                                 ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#max_normal_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#variants> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#germline_hc> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#somatic_hc> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#loh> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#germline> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#loh_hc> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#somatic> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_base_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cle_vcf_filter>
        cwl:default  false ;
        sld:type     xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_readgroups>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/qc_minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#qc_minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#panel_of_normals_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/hs_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl#output_vcf_basename>
        cwl:default  "select_variants" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_ensembl_species>
        rdfs:comment  "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#sample>
        cwl:inputBinding  [ CommandLineBinding:position
                          -6 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          -6 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/dbsnp_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#dbsnp_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(self.basename)"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_p_value>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_p_value> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/metric_accumulation_level>
        cwl:valueFrom  "ALL_READS" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#select_variants/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#omni_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter/variant_caller>
        cwl:valueFrom  "strelka" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "strelka workflow" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#merge> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#index_full> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#process> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#region_filter> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#exome_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#cpu_reserved> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#interval_list> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#unfiltered_vcf> ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#tumor_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/bait_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#bait_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/per_target_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#per_target_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter/variant_caller> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter/filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter/unfiltered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/unfiltered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance/bam_2>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/custom_gnomad_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#custom_gnomad_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/per_base_coverage>
        cwl:default  false .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/min_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#readcount_minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_insert_size_metrics.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "REFERENCE_SEQUENCE=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "REFERENCE_SEQUENCE=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#insert_size>
        cwl:default  400 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#merge>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#merge/vcfs> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#merge/merged_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#normalize_variants/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#cosmic_vcf>
        cwl:inputBinding    [ CommandLineBinding:position  6 ;
                              CommandLineBinding:prefix    "--cosmic"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/bam_readcount_tsv>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#snv_bam_readcount_tsv> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#sample_name>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-s" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-s" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-s" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-s" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl#normal_bam>
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "-I"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "exome alignment and somatic variant detection" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_index_cram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bam_to_cram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_index_cram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_bam_to_cram> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#somalier_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#strelka_cpu_reserved> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_cache_dir> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#omni_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#qc_minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_artifact_detection_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_ensembl_species> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#panel_of_normals_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#summary_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_readgroups> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mills> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#custom_gnomad_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#qc_minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#annotate_coding_only> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta_output_contigs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_max_normal_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#picard_metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_bams> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_ensembl_version> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#custom_clinvar_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_max_alt_allele_in_normal_fraction> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#per_base_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_scatter_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_max_alt_alleles_in_normal_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#synonyms_file> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#variants_to_table_genotype_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_p_value> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#bqsr_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cle_vcf_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_strand_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_readgroups> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cosmic_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_min_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#known_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_ensembl_assembly> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bams> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#variants_to_table_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#filter_docm_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#pindel_insert_size> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#docm_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta_call_regions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_to_table_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta_non_wgs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#per_target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#target_intervals> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_antitarget_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_per_target_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cn_diagram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#strelka_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_verify_bam_id_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#strelka_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_target_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#all_candidates> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#small_candidates> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_mark_duplicates_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#somalier_concordance_statistics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_summary> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_summary_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bin_level_ratios> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_verify_bam_id_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_summary_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#intervals_target> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_per_target_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#somatic_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#intervals_antitarget> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#somalier_concordance_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_flagstats> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#docm_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#diploid_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_only_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_flagstats> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_cram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cn_scatter_plot> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_antitarget_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_summary_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_summary_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#final_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_segmented_ratios> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#pindel_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#final_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#final_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#pindel_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_mark_duplicates_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_cram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#reference_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_target_coverage> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a                           cwl:SchemaDefRequirement ;
                                   SchemaDefRequirement:types  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file>
                                 ] ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#intervals_to_bed/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#name_sort>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#name_sort/bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#name_sort/name_sorted_bam> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/name_sort.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_base_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_base_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_target_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_target_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc_minimum_base_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#merge>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#merge/bams> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#merge/name> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#merge/merged_bam> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_bams_samtools.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#bgzip2/file>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_filter/docm_filtered_variants> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#synonyms_file>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#omni_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#summary_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/ensembl_version>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_ensembl_version> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/bait_intervals>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_target_intervals> ;
        cwl:valueFrom  "$(self.file)" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/apply_bqsr.cwl#bqsr_table>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-BQSR"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-BQSR"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#tumor_bam>
        cwl:inputBinding    [ CommandLineBinding:position  3 ;
                              CommandLineBinding:prefix    "--tumorBam=" ;
                              CommandLineBinding:separate  false
                            ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_base_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/per_base_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/summary_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#summary_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#readcount_minimum_base_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/data_type>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/omni_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#omni_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/sample_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/variant_type> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/data_type> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/bam_readcount_tsv> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/annotated_bam_readcount_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          -7 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          -7 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_snv_bam_readcount_tsv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/tumor_snv_bam_readcount_tsv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics>
        cwl:in             <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/per_target_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/output_prefix> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/per_base_coverage> ;
        cwl:out            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/hs_metrics> ;
        cwl:run            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/bait_intervals> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/target_intervals> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/output_prefix> ) ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/bait_intervals> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/target_intervals> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/output_prefix> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#normal_bam>
        cwl:inputBinding    [ CommandLineBinding:position  -2 ;
                              CommandLineBinding:prefix    "--normalBam"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/cpu_reserved> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/exome_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/normal_bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/unfiltered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/known_indels>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#known_indels> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#final_bam>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#index_bam/indexed_bam> ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_name>
        cwl:default  "tumor" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/ensembl_assembly>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_ensembl_assembly> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_strand_filter>
        cwl:default  0 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mills>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#output_prefix>
        cwl:default  "out" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#merge/merged_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/per_target_coverage>
        cwl:default  true .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#minimum_mapping_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "pindel parallel workflow" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#somaticfilter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#reindex> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#index> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#remove_end_tags> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#cat_all> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#region_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#bgzip> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#get_chromosome_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#insert_size> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#tumor_bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#unfiltered_vcf> ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#normal_bam>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "--normal"
                          ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table/genotype_fields>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table_genotype_fields> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf/snv_bam_readcount_tsv>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/snv_bam_readcount_tsv> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#synonyms_file>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/custom_clinvar_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#custom_clinvar_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#picard_metric_accumulation_level>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/strand_filter>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_strand_filter> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_ensembl_assembly>
        rdfs:comment  "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_insert_size_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/insert_size_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#max_normal_freq>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "--max-normal-freq"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "--max-normal-freq"
                          ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#decompose_variants/decomposed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/variant_caller>
        cwl:valueFrom  "varscan" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#somatic_variants>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "results/variants/somaticSV.vcf.gz" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "CombineVariants (GATK 3.6)" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-genotypeMergeOptions" "PRIORITIZE" "--rod_priority_list" "mutect,varscan,strelka,pindel" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/combined.vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl#pindel_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl#varscan_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl#mutect_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl#strelka_vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl#combined_vcf> ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     9000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_per_target_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_target_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/unfiltered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#interval_list>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/gatherer.cwl#gathered_files>
        cwl:outputBinding  [ CommandOutputBinding:outputEval
                          "${ var file_paths = []; var new_path = inputs.output_dir; if (new_path.slice(-1) != \"/\") { new_path += \"/\"; } var arrLen = inputs.all_files.length; for(var i = 0; i < arrLen; i++) { file_paths.push(new_path + inputs.all_files[i].basename); } return file_paths; }" ] ;
        sld:type           [ sld:items  xsd:string ;
                             sld:type   sld:array
                           ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/max_normal_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/variants> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/germline_hc> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/loh_hc> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/somatic> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/loh> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/somatic_hc> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/germline> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#cle_vcf_filter>
        cwl:default  false ;
        sld:type     xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/docm_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/docm_raw_variants> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_bams>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#tumor_bams> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/max_normal_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#max_normal_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/variant_caller> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/apply_bqsr.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "apply BQSR" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_name)" ]
                                   "-preserveQ" "6" "-SQQ" "10" "-SQQ" "20" "-SQQ" "30" "-nct" "8" "--disable_indel_quals"
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_name)" ]
                                   "-preserveQ" "6" "-SQQ" "10" "-SQQ" "20" "-SQQ" "30" "-nct" "8" "--disable_indel_quals"
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "PrintReads" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "PrintReads" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/apply_bqsr.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/apply_bqsr.cwl#bqsr_table> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/apply_bqsr.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/apply_bqsr.cwl#output_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/apply_bqsr.cwl#bqsr_bam> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  18000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  18000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/sample_names>
        cwl:default  "NORMAL,TUMOR" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#interval_list>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr/known_sites> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr/intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr/bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr/bqsr_table> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bqsr.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/min_coverage>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#min_coverage> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#scatter_plot>
        cwl:inputBinding  [ CommandLineBinding:position  8 ;
                            CommandLineBinding:prefix    "--scatter"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_cram_name>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#tumor_cram_name> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/insert_size> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/chromosome> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/tumor_bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/insertions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/long_insertions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/deletions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/tandems> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/inversions> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#bgzip2>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#bgzip2/file> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#bgzip2/bgzipped_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bgzip.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/output_prefix>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#summary_intervals> ;
        cwl:valueFrom  "summary-$(self.label)" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#picard_metric_accumulation_level>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#index>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#index/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#index/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/mutect_filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/min_var_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#min_var_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#normal_bam>
        cwl:inputBinding    [ CommandLineBinding:position  4 ;
                              CommandLineBinding:prefix    "--normalBam=" ;
                              CommandLineBinding:separate  false
                            ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/output_vcf_basename>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#variant_caller> ;
        cwl:valueFrom  "$(self)_full" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#hard_filter>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#hard_filter/exclude_filtered> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#hard_filter/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#hard_filter/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#hard_filter/output_vcf_basename> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#hard_filter/filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_pick>
        sld:type  sld:null ;
        sld:type  [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_pick/flag_pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_pick/flag_pick_allele> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_pick/flag_pick_allele_gene> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_pick/per_gene> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_pick/pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_pick/pick_allele> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_pick/pick_allele_gene> ;
                    sld:type     sld:enum
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_snvs/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_snvs/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mills>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/readgroups> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/picard_metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bams> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/qc_minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/qc_minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/omni_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bqsr_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/summary_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_base_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/known_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/mills> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/final_name> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/alignment_summary_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/mark_duplicates_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_target_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/summary_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/flagstats> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/verify_bam_id_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/insert_size_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/target_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#target_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#remove_end_tags>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#remove_end_tags/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#remove_end_tags/processed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/remove_end_tags.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_filter/filter_docm_variants>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#filter_docm_variants> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#final_name>
        cwl:default  "final.bam" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta_output_contigs>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#variants_to_table_genotype_fields>
        cwl:default  "AD" , "GT" ;
        sld:type     [ sld:items  xsd:string ;
                       sld:type   sld:array
                     ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/omni_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#omni_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-t" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-t" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-t" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-t" ] ;
        sld:type          sld:null ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type/all> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type/indel> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type/snv> ;
                            sld:type     sld:enum
                          ] ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type/all> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type/indel> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type/snv> ;
                            sld:type     sld:enum
                          ] ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type/all> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type/indel> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type/snv> ;
                            sld:type     sld:enum
                          ] ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type/all> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type/indel> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type/snv> ;
                            sld:type     sld:enum
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/data_type> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/sample_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/variant_type> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/bam_readcount_tsv> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/annotated_bam_readcount_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#pindel_insert_size>
        cwl:default  400 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter/unfiltered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc_minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_insert_size_metrics.cwl#metric_accumulation_level>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#roi_bed>
        cwl:inputBinding  [ CommandLineBinding:position
                          8 ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/apply_bqsr.cwl#bqsr_bam>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#cle_vcf_filter>
        cwl:default  false ;
        sld:type     xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_name>
        cwl:default  "normal" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#summary_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#index2>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#index2/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#index2/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#align_and_tag/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#select_variants>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#select_variants/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#select_variants/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#select_variants/interval_list> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#select_variants/filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_p_value>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_p_value> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#qc_minimum_base_quality>
        cwl:default  0 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_cache_dir>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_index/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#custom_gnomad_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic_snvs>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/somatic> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "exome alignment with qc" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#summary_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#bqsr_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#readgroups> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#mills> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#final_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc_minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#picard_metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#known_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_base_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc_minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#omni_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#bams> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#summary_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#verify_bam_id_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment_summary_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#insert_size_histogram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#flagstats> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#mark_duplicates_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_target_hs_metrics> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a                           cwl:SchemaDefRequirement ;
                                   SchemaDefRequirement:types  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file>
                                 ] ;
        cwl:requirements         [ a                           cwl:SchemaDefRequirement ;
                                   SchemaDefRequirement:types  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file>
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table_genotype_fields>
        cwl:default  "AD" , "GT" ;
        sld:type     sld:null ;
        sld:type     [ sld:items  xsd:string ;
                       sld:type   sld:array
                     ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#variants_to_table_fields>
        cwl:default  "AC" , "ID" , "ALT" , "CHROM" , "POS" , "REF" , "set" , "AF" ;
        sld:type     [ sld:items  xsd:string ;
                       sld:type   sld:array
                     ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/per_base_coverage>
        cwl:default  false .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#decompose_index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#decompose/decomposed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_vcf.cwl#merged_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.merged_vcf_basename).vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.merged_vcf_basename).vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.merged_vcf_basename).vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/output_prefix>
        cwl:valueFrom  "roi" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_target_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_target_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#summary_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#min_base_quality>
        cwl:default       20 ;
        cwl:inputBinding  [ CommandLineBinding:position
                          -2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          -2 ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#bgzip/bgzipped_file> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_target_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_target_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/variants_to_table.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine/strelka_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#summary_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/summary_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/variants_to_table_genotype_fields>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#variants_to_table_genotype_fields> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/min_var_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#min_var_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/variants_to_table.cwl#fields>
        cwl:default       "ID" , "ALT" , "CHROM" , "POS" , "REF" , "set" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          [ cwl:inputBinding  [ CommandLineBinding:prefix
                                              "-F" ] ;
                            sld:items         xsd:string ;
                            sld:type          sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#insert_size_histogram>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/insert_size_histogram> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#insert_size_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/insert_size_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-f" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/samtools_flagstat.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "samtools flagstat" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/samtools/bin/samtools" "flagstat" ) ;
        cwl:baseCommand          ( "/opt/samtools/bin/samtools" "flagstat" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/samtools_flagstat.cwl#bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/samtools_flagstat.cwl#flagstats> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:stdout               "$(inputs.bam.basename).flagstat" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/split_interval_list.cwl#scatter_count>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "SCATTER_COUNT=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#minimum_base_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type>
        sld:type  [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type/DNA> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type/RNA> ;
                    sld:type     sld:enum
                  ] ;
        sld:type  [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type/DNA> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type/RNA> ;
                    sld:type     sld:enum
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#panel_of_normals_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#known_indels>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#pindel_filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/pindel_filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine/mutect_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine/pindel_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine/strelka_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine/varscan_vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine/combined_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl#bam_1>
        cwl:inputBinding    [ CommandLineBinding:position
                          3 ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#interval_list>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#tumor_segmented_ratios>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.tumor_bam.nameroot).cns" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/mutect_scatter_count>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_scatter_count> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#interval_list>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_cache_dir>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_vcf.cwl#vcfs>
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            [ sld:items  cwl:File ;
                              sld:type   sld:array
                            ] ;
        sld:type            [ sld:items  cwl:File ;
                              sld:type   sld:array
                            ] ;
        sld:type            [ sld:items  cwl:File ;
                              sld:type   sld:array
                            ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/metric_accumulation_level>
        cwl:valueFrom  "ALL_READS" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_base_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_base_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somalier_vcf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#male_reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-y" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#variant_caller>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#pindel_unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/pindel_unfiltered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_vep_fields_to_table.cwl#vep_fields>
        cwl:default       "Consequence" , "Feature" , "SYMBOL" , "HGVSp" , "HGVSc" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#cat/pindel_outs>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/deletions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/insertions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/inversions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/long_insertions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/tandems> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#omni_vcf>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/max_normal_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#max_normal_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#region_filter>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#region_filter/interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#region_filter/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#region_filter/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#region_filter/filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#bam>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/mutect_max_alt_allele_in_normal_fraction>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_max_alt_allele_in_normal_fraction> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/output_vcf_basename> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/sample_name> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mutect_scatter_count>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mutect_scatter_count> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_max_normal_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_max_normal_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_flagstats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/flagstats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/synonyms_file>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#synonyms_file> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "collect HS metrics" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
                                 ) ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
                                 ) ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
                                 ) ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
                                 ) ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
                                 ) ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
                                 ) ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
                                 ) ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#per_base_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#output_prefix> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#per_target_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#minimum_mapping_quality> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#hs_metrics> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  52000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  52000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  52000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  52000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  52000
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  52000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  52000
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  52000
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_target_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#per_target_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/min_var_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#min_var_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#vcf>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "mutect.vcf.gz" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/docm_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#docm_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/variants_to_table.cwl#variants_tsv>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "variants.tsv" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect>
        cwl:in       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/cosmic_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/artifact_detection_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/panel_of_normals_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/max_alt_allele_in_normal_fraction> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/max_alt_alleles_in_normal_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/dbsnp_vcf> ;
        cwl:out      <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/vcf> ;
        cwl:run      <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl> ;
        cwl:scatter  ( <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/interval_list> ) .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/filter_somatic_llr_threshold>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_somatic_llr_threshold> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mutect_max_alt_alleles_in_normal_count>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mutect_max_alt_alleles_in_normal_count> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/strelka_exome_mode>
        cwl:default  true .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#tumor_cram_name>
        cwl:default  "tumor.cram" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#max_alt_alleles_in_normal_count>
        cwl:inputBinding  [ CommandLineBinding:position  9 ;
                            CommandLineBinding:prefix    "--max_alt_alleles_in_normal_count"
                          ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_unfiltered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_index_cram/cram>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_bam_to_cram/cram> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_indels>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_indels/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_indels/filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_indels/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_indels/merged_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/set_filter_status.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bam_to_cram/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#interval_list>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_max_alt_alleles_in_normal_count>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#max_alt_alleles_in_normal_count>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#bam>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#omni_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl#varscan_vcf>
        cwl:inputBinding    [ CommandLineBinding:position  3 ;
                              CommandLineBinding:prefix    "--variant:varscan"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf/sample_name>
        cwl:default  "TUMOR" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#decompose_index>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#decompose_index/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#decompose_index/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_cle.cwl#vcf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_ensembl_species>
        rdfs:comment  "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cat_all.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  "|"
                                   ]
                                   "/bin/grep" "ChrID" "/dev/stdin"
                                 ) ;
        cwl:baseCommand          ( "/bin/cat" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cat_all.cwl#chromosome_pindel_outs> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cat_all.cwl#all_chromosome_pindel_head> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "ubuntu:xenial"
                                 ] ;
        cwl:stdout               "all_chromosome_pindel.head" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_cle>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_cle/filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_cle/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_cle/cle_filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_cle.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#normal_cram_name>
        cwl:default  "normal.cram" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/set_filter_status.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "create filtered VCF" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "--maskName" "processSomatic" "--filterNotInMask" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/output.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "--maskName" "processSomatic" "--filterNotInMask" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/output.vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantFiltration" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantFiltration" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/set_filter_status.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/set_filter_status.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/set_filter_status.cwl#filtered_vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/set_filter_status.cwl#merged_vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_alignment_summary_metrics.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "REFERENCE_SEQUENCE=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "REFERENCE_SEQUENCE=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_verify_bam_id_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/verify_bam_id_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#qc_minimum_mapping_quality>
        cwl:default  0 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bams>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-i"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#tumor_bam>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#tumor_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/final_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mutect_max_alt_allele_in_normal_fraction>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_bgzip/bgzipped_file> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_p_value>
        cwl:default  9.9e-01 ;
        sld:type     xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/dbsnp_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#dbsnp_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:position  3 ;
                              CommandLineBinding:prefix    "-I"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/remove_end_tags.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "remove END INFO tags" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-x" "INFO/END" "-Oz" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/pindel.noend.vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "/opt/bcftools/bin/bcftools" "annotate" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/remove_end_tags.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/remove_end_tags.cwl#processed_vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-s"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#per_base_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#normal_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf/indel_bam_readcount_tsv>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/indel_bam_readcount_tsv> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#per_target_coverage>
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_TARGET_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_TARGET_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_TARGET_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_TARGET_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_TARGET_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_TARGET_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_TARGET_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_TARGET_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#flagstats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#samtools_flagstat/flagstats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_filter/docm_raw_variants>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#decompose/decomposed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#target_intervals>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "TARGET_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "TARGET_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "TARGET_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "TARGET_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "TARGET_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "TARGET_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "TARGET_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "TARGET_INTERVALS=" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/dbsnp_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#dbsnp_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_target_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#per_target_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_snv_bam_readcount_tsv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/snv_bam_readcount_tsv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_per_target_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_target_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#tumor_bam>
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#region_filter/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#index/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel_somatic_filter.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "pindel somatic filter v1" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "/usr/bin/perl" "/usr/bin/write_pindel_filter_config.pl" "$(inputs.pindel_output_summary.path)" "$(inputs.reference)" "$(runtime.outdir)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/usr/bin/perl" "/usr/bin/somatic_indelfilter.pl" "filter.config"
                                 ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel_somatic_filter.cwl#pindel_output_summary> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel_somatic_filter.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel_somatic_filter.cwl#vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  16000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "--reference"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "--reference"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "--reference"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "--reference"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_somatic_llr.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          -1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/align_and_tag.cwl#readgroup>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_min_var_freq>
        cwl:default  5e-02 ;
        sld:type     xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#bgzip>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#bgzip/file> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#bgzip/bgzipped_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bgzip.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#normal_bams>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/custom_clinvar_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#custom_clinvar_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_somatic_llr_threshold>
        cwl:default  5 ;
        sld:type     xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table_fields>
        cwl:default  "CHROM" , "ID" , "AF" , "REF" , "AC" , "ALT" , "set" , "POS" ;
        sld:type     sld:null ;
        sld:type     [ sld:items  xsd:string ;
                       sld:type   sld:array
                     ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic_hc_snvs>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/somatic_hc> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/target_intervals>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_base_intervals> ;
        cwl:valueFrom  "$(self.file)" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#strand_filter>
        cwl:default       0 ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#region_filter>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#region_filter/interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#region_filter/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#region_filter/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#region_filter/filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#mark_duplicates_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/mark_duplicates_metrics_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#insert_size>
        cwl:default  400 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_to_cram.cwl#cram>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).cram" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).cram" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#snv_bam_readcount_tsv>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sample)_bam_readcount_snv.tsv" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sample)_bam_readcount_snv.tsv" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#tumor_only_variants>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "results/variants/tumorSV.vcf.gz" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/filter_docm_variants>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#filter_docm_variants> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Concordance checking between Tumor and Normal BAM" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-o" "concordance" ) ;
        cwl:baseCommand          ( "/usr/bin/somalier" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl#bam_2> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl#bam_1> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl#somalier_samples> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl#somalier_pairs> ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:ramMin     8000 ;
                                   ResourceRequirement:tmpdirMin  10000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "brentp/somalier:v0.1.5"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#index_full/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#merge/merged_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl#indexed_vcf>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.vcf.basename)" ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/gatherer.cwl#output_dir>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/set_filter_status.cwl#filtered_vcf>
        cwl:inputBinding    [ CommandLineBinding:position  3 ;
                              CommandLineBinding:prefix    "--mask"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  3 ;
                              CommandLineBinding:prefix    "--mask"
                            ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/variants_to_table_fields>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#variants_to_table_fields> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/dbsnp_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#dbsnp_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter/variant_caller>
        cwl:valueFrom  "mutect" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "-f"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#normal_antitarget_coverage>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "${\n    var glob_base = \".antitargetcoverage.cnn\";\n    if (inputs.normal_bam) {\n        glob_base = inputs.normal_bam.nameroot + glob_base;\n    }\n    return glob_base;\n}\n" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf/snv_bam_readcount_tsv>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/snv_bam_readcount_tsv> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc_minimum_base_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_depth.cwl#sample_names>
        cwl:inputBinding  [ CommandLineBinding:position
                          -1 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_mark_duplicates_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/mark_duplicates_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_pick>
        sld:type  sld:null ;
        sld:type  [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_pick/flag_pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_pick/flag_pick_allele> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_pick/flag_pick_allele_gene> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_pick/per_gene> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_pick/pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_pick/pick_allele> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_pick/pick_allele_gene> ;
                    sld:type     sld:enum
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_summary>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/vep_summary> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_vep_fields_to_table.cwl#prefix>
        cwl:default  "variants" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/per_base_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#per_base_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_gnomADe_allele_freq.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-i"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl#filtered_vcf>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf.gz" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf.gz" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf.gz" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf.gz" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf.gz" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf.gz" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf.gz" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf.gz" ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_bgzip/bgzipped_file> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter/variant_caller> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter/filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter/unfiltered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#index_bam>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#index_bam/bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#index_bam/indexed_bam> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_bam.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_ensembl_version>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_ensembl_version> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#loh_hc>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.LOH.hc.vcf" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.LOH.hc.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_target_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/per_target_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge/merged_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#decompose/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#index/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#dbsnp_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_mapq0/threshold>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_mapq0_threshold> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_indels/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/somatic_indels> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#hs_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#summary_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#minimum_base_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/cosmic_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/max_alt_allele_in_normal_fraction> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/panel_of_normals_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/max_alt_alleles_in_normal_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/scatter_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/artifact_detection_mode> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#non_wgs>
        rdfs:comment      "toggles on settings for WES" ;
        cwl:inputBinding  [ CommandLineBinding:position  -6 ;
                            CommandLineBinding:prefix    "--exome"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_max_alt_allele_in_normal_fraction>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#data_type>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#data_type/DNA> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#data_type/RNA> ;
                            sld:type     sld:enum
                          ] ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#data_type/DNA> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#data_type/RNA> ;
                            sld:type     sld:enum
                          ] ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#data_type/DNA> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#data_type/RNA> ;
                            sld:type     sld:enum
                          ] ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#data_type/DNA> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#data_type/RNA> ;
                            sld:type     sld:enum
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "mutect2 (GATK 3.6)" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/mutect.vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "MuTect2" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#artifact_detection_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#panel_of_normals_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#max_alt_allele_in_normal_fraction> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#max_alt_alleles_in_normal_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#cosmic_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#normal_bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     20000 ;
                                   ResourceRequirement:tmpdirMin  100000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#final_tsv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/final_tsv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#indels>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "output.indel.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_bam_to_cram/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#intervals_to_bed>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#intervals_to_bed/interval_list> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#intervals_to_bed/interval_bed> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/intervals_to_bed.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--referenceFasta=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#max_normal_freq>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_indel_bam_readcount_tsv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/indel_bam_readcount_tsv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/set_filter_status.cwl#merged_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "output.vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "output.vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#normalize_variants/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/insert_size_histogram> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_insert_size_metrics.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#samtools_flagstat/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/verify_bam_id.cwl#verify_bam_id_depth>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).VerifyBamId.depthSM" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).VerifyBamId.depthSM" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#normalize_variants>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#normalize_variants/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#normalize_variants/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#normalize_variants/normalized_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/normalize_variants.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#target_intervals>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/per_base_coverage>
        cwl:default  true .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_mapq0_threshold>
        cwl:default  1.5e-01 ;
        sld:type     xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/readgroups>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_readgroups> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#split_interval_list/scatter_count>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#scatter_count> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/per_base_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_base_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#cache_dir>
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--dir"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_snvs/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/somatic_snvs> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#known_indels>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_insert_size_metrics.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/non_wgs>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta_non_wgs> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mark_duplicates_and_sort/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#name_sort/name_sorted_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/panel_of_normals_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#panel_of_normals_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_cle/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_mapq0/mapq0_filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/annotated_bam_readcount_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#align_and_tag/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/bait_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#bait_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf/indel_bam_readcount_tsv>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/indel_bam_readcount_tsv> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/picard_metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_base_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/known_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/final_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bams> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/readgroups> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/qc_minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/summary_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bqsr_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/omni_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/qc_minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/mills> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/verify_bam_id_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/alignment_summary_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_target_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/mark_duplicates_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/flagstats> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/summary_hs_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/insert_size>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel_insert_size> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr/known_sites>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mills> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#known_indels> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#hard_filter/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_index/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/mills>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mills> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/panel_of_normals_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#panel_of_normals_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#readcount_minimum_mapping_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#min_var_freq>
        cwl:default       1e-01 ;
        cwl:inputBinding  [ CommandLineBinding:position
                          6 ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/p_value>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#p_value> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/name_sort.cwl#bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/variants_to_table.cwl#vcf>
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#tumor_bam>
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "-I:tumor"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_vcf.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "vcf merge" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "/opt/bcftools/bin/bcftools" "concat" ) ;
        cwl:baseCommand          ( "/opt/bcftools/bin/bcftools" "concat" ) ;
        cwl:baseCommand          ( "/opt/bcftools/bin/bcftools" "concat" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_vcf.cwl#vcfs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_vcf.cwl#merged_vcf_basename> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_vcf.cwl#merged_vcf> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#bgzip/file>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#somaticfilter/vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics>
        cwl:in             <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/per_base_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/output_prefix> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/per_target_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/target_intervals> ;
        cwl:out            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/hs_metrics> ;
        cwl:run            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/bait_intervals> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/target_intervals> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/output_prefix> ) ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/bait_intervals> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/target_intervals> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/output_prefix> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_vep_fields_to_table/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_index/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/apply_bqsr.cwl#output_name>
        cwl:default  "Final.bam" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#dbsnp_vcf>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/annotated_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/panel_of_normals_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#panel_of_normals_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#output_dir>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#strelka_filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/strelka_filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/bait_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#bait_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#name_sort/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#merge/merged_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#dbsnp_vcf>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_gnomADe_allele_freq/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#inversions>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "all_INV" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "fp_filter workflow" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#index> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_bgzip> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#decompose_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#hard_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#normalize_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_index> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#sample_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#variant_caller> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#filtered_vcf> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/samtools_flagstat.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_mapq0_threshold>
        sld:type  xsd:float .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_vep_fields_to_table>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_vep_fields_to_table/vep_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_vep_fields_to_table/tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_vep_fields_to_table/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_vep_fields_to_table/annotated_variants_tsv> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_vep_fields_to_table.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#interval_list>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#align_and_tag>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#align_and_tag/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#align_and_tag/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#align_and_tag/readgroup> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#align_and_tag/aligned_bam> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/align_and_tag.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_cle.cwl#filter>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "filter"
                          ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "SelectVariants (GATK 3.6)" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl#exclude_filtered> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl#interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl#output_vcf_basename> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl#filtered_vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/sample_name>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#sample_name> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bqsr.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "create BQSR table" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/bqsr.table" ]
                                   "--preserve_qscores_less_than" "6" "--disable_auto_index_creation_and_locking_when_reading_rods" "--disable_bam_indexing" "-dfrac" ".1" "-nct" "4"
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/bqsr.table" ]
                                   "--preserve_qscores_less_than" "6" "--disable_auto_index_creation_and_locking_when_reading_rods" "--disable_bam_indexing" "-dfrac" ".1" "-nct" "4"
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "BaseRecalibrator" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "BaseRecalibrator" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bqsr.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bqsr.cwl#intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bqsr.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bqsr.cwl#known_sites> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bqsr.cwl#bqsr_table> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  18000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  18000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bqsr.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/p_value>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#p_value> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#index/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "HS Metrics workflow" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_base_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#summary_intervals> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_target_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#summary_hs_metrics> ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a                           cwl:SchemaDefRequirement ;
                                   SchemaDefRequirement:types  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file>
                                 ] ;
        cwl:requirements         [ a                           cwl:SchemaDefRequirement ;
                                   SchemaDefRequirement:types  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file>
                                 ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/bam_readcount_tsv>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#indel_bam_readcount_tsv> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_docm.cwl#docm_raw_variants>
        cwl:inputBinding  [ CommandLineBinding:position
                          -4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_cram.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "samtools index cram" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.cram.basename)" "$(runtime.outdir)/$(inputs.cram.basename).crai"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "cp" "$(inputs.cram.basename).crai" "$(runtime.outdir)/$(inputs.cram.nameroot).crai"
                                 ) ;
        cwl:arguments            ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.cram.basename)" "$(runtime.outdir)/$(inputs.cram.basename).crai"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "cp" "$(inputs.cram.basename).crai" "$(runtime.outdir)/$(inputs.cram.nameroot).crai"
                                 ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_cram.cwl#cram> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_cram.cwl#indexed_cram> ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.cram)"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.cram)"
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#normal_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align>
        cwl:in             <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align/readgroup> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align/reference> ;
        cwl:out            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align/tagged_bam> ;
        cwl:run            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align/bam> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align/readgroup> ) ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align/bam> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align/readgroup> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Set up and execute manta" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  -1 ;
                                     CommandLineBinding:prefix    "--runDir" ;
                                     cwl:valueFrom                "$(runtime.outdir)"
                                   ]
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  "&&"
                                   ]
                                   "/usr/bin/python" "runWorkflow.py" "-m" "local"
                                   [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-j" ;
                                     cwl:valueFrom                "$(runtime.cores)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/python" "/usr/bin/manta/bin/configManta.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#non_wgs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#call_regions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#output_contigs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#normal_bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#tumor_only_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#small_candidates> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#all_candidates> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#somatic_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#diploid_variants> ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   12 ;
                                   ResourceRequirement:ramMin     24000 ;
                                   ResourceRequirement:tmpdirMin  10000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/manta_somatic-cwl:1.5.0"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/mutect_unfiltered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_depth.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "filter variants at sites below a given sequence depth in each sample" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ cwl:valueFrom  "$(runtime.outdir)/depth_filtered.vcf" ]
                                 ) ;
        cwl:baseCommand          ( "/opt/conda/bin/python3" "/usr/bin/depth_filter.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_depth.cwl#minimum_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_depth.cwl#sample_names> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_depth.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_depth.cwl#depth_filtered_vcf> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/depth-filter:0.1"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_strand_filter>
        cwl:default  0 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#index_full>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#index_full/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#index_full/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#region_filter/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#index_full/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_docm.cwl#normal_bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          -3 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_snvs>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_snvs/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_snvs/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mark_duplicates_metrics_file>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mark_duplicates_and_sort/metrics_file> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_hc_snvs>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_hc_snvs/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_hc_snvs/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#per_chromosome_pindel_out>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#cat/pindel_out> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#cat_all>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#cat_all/chromosome_pindel_outs> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#cat_all/all_chromosome_pindel_head> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cat_all.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_docm_variants/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#germline_indels>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/germline> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_scatter_count>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#panel_of_normals_vcf>
        cwl:inputBinding    [ CommandLineBinding:position  8 ;
                              CommandLineBinding:prefix    "-PON"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#chromosome>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mills>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#somalier_concordance_statistics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance/somalier_samples> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_per_base_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_base_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel_filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Per-chromosome pindel" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#cat> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#insert_size> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#chromosome> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#per_chromosome_pindel_out> ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/target_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#target_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/get_chromosome_list.cwl#chromosome_list>
        cwl:outputBinding  [ CommandOutputBinding:glob  "chromosome.list" ;
                             CommandOutputBinding:outputEval
                                     "$( self[0].contents.split(\"\\n\").slice(0, -1))" ;
                             cwl:loadContents           true
                           ] ;
        sld:type           [ sld:items  xsd:string ;
                             sld:type   sld:array
                           ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/variant_type>
        cwl:default  "snv" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_snvs/filtered_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_hc_snvs/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/bait_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#bait_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_index_cram>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_index_cram/cram> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_index_cram/indexed_cram> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_cram.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#bam>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/final_bam> ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#tumor_bin_level_ratios>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.tumor_bam.nameroot).cnr" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vt_decompose.cwl#vcf>
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/per_base_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/summary_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/picard_metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/omni_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/per_target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/flagstats> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/summary_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/per_target_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/verify_bam_id_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/alignment_summary_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/insert_size_histogram> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cn_scatter_plot>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/cn_scatter_plot> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/synonyms_file>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#synonyms_file> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/cpu_reserved>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#cpu_reserved> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mark_duplicates_and_sort.cwl#bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#min_var_freq>
        cwl:default       5e-02 ;
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--min-var-freq"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--min-var-freq"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--min-var-freq"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--min-var-freq"
                          ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/cpu_reserved> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/exome_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/snvs> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#artifact_detection_mode>
        cwl:inputBinding  [ CommandLineBinding:position  7 ;
                            CommandLineBinding:prefix    "--artifact_detection_mode"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#exome_mode>
        cwl:inputBinding  [ CommandLineBinding:position  6 ;
                            CommandLineBinding:prefix    "--exome"
                          ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mutect_artifact_detection_mode>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mutect_artifact_detection_mode> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#small_candidates>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "results/variants/candidateSmallIndels.vcf.gz" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#strelka_cpu_reserved>
        cwl:default  8 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#bgzip/bgzipped_file> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_ensembl_assembly>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_ensembl_assembly> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#metric_accumulation_level>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#hard_filter/filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge/vcfs>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index_indels/indexed_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index_snvs/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bgzip.cwl#bgzipped_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.file.basename).gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#bgzip/file>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/docm_raw_variants> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_cle/cle_filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/samtools_flagstat.cwl#flagstats>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.basename).flagstat" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.basename).flagstat" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_max_normal_freq>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bgzip.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "bgzip VCF" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-c" ) ;
        cwl:arguments            ( "-c" ) ;
        cwl:arguments            ( "-c" ) ;
        cwl:arguments            ( "-c" ) ;
        cwl:arguments            ( "-c" ) ;
        cwl:arguments            ( "-c" ) ;
        cwl:arguments            ( "-c" ) ;
        cwl:arguments            ( "-c" ) ;
        cwl:arguments            ( "-c" ) ;
        cwl:arguments            ( "-c" ) ;
        cwl:arguments            ( "-c" ) ;
        cwl:arguments            ( "-c" ) ;
        cwl:arguments            ( "-c" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:baseCommand          ( "/opt/htslib/bin/bgzip" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bgzip.cwl#file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bgzip.cwl#bgzipped_file> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:stdout               "$(inputs.file.basename).gz" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#sample_name>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#diploid_variants>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "results/variants/diploidSV.vcf.gz" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/mutect_scatter_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/custom_clinvar_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_ensembl_species> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_cache_dir> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/mutect_artifact_detection_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/mutect_max_alt_alleles_in_normal_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_to_table_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/pindel_insert_size> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/strelka_exome_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/annotate_coding_only> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/strelka_cpu_reserved> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/panel_of_normals_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_ensembl_assembly> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/docm_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/custom_gnomad_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_strand_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/synonyms_file> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_ensembl_version> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_max_normal_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/mutect_max_alt_allele_in_normal_fraction> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_min_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/filter_docm_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/cosmic_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/variants_to_table_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/cle_vcf_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_p_value> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/variants_to_table_genotype_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_pick> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/tumor_snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/final_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_summary> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/tumor_indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/mutect_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/strelka_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/pindel_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/normal_indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/normal_snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/mutect_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/final_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/pindel_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/final_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/strelka_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/docm_filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/max_alt_allele_in_normal_fraction>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#max_alt_allele_in_normal_fraction> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_ensembl_assembly>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_ensembl_assembly> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Varscan Workflow" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#intervals_to_bed> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_hc_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index_snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_hc_snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_snvs> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#max_normal_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#p_value> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#strand_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#min_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filtered_vcf> ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/get_chromosome_list.cwl#interval_list>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_gnomADe_allele_freq>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_gnomADe_allele_freq/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_gnomADe_allele_freq/maximum_population_allele_frequency> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_gnomADe_allele_freq/filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_gnomADe_allele_freq.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#custom_clinvar_vcf>
        cwl:inputBinding    [ CommandLineBinding:position  7 ;
                              cwl:valueFrom                "${\n    if (inputs.custom_clinvar_vcf) {\n        return [\"--custom\", inputs.custom_clinvar_vcf.path + \",clinvar,vcf,exact,0,CLINSIGN,PHENOTYPE,SCORE,RCVACC,TESTEDINGTR,PHENOTYPELIST,NUMSUBMIT,GUIDELINES\"]\n\n    }\n    else {\n        return []\n    }\n}\n"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/hgvs_annotation>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#hgvs_annotation> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl#vcf>
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#tagged_bam>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#align_and_tag/aligned_bam> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#bgzip>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#bgzip/file> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#bgzip/bgzipped_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bgzip.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_readgroups>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#tumor_readgroups> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/target_intervals>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#summary_intervals> ;
        cwl:valueFrom  "$(self.file)" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#final_outputs>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#gatherer/gathered_files> ;
        sld:type          [ sld:items  xsd:string ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#cpu_reserved>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc_minimum_mapping_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--vcf-file"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--vcf-file"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--vcf-file"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--vcf-file"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index_snvs/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_snvs/merged_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/strand_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/roi_bed> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/p_value> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/max_normal_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/min_coverage> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/somatic_hc_snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/somatic_snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/somatic_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/somatic_hc_indels> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_vep_fields_to_table.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_vep_fields_to_table/vep_fields>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_to_table_fields> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#normal_target_coverage>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "${\n    var glob_base = \".targetcoverage.cnn\";\n    if (inputs.normal_bam) {\n        glob_base = inputs.normal_bam.nameroot + glob_base;\n    }\n    return glob_base;\n}\n" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#annotated_bam_readcount_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "annotated.bam_readcount.vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "annotated.bam_readcount.vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "annotated.bam_readcount.vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "annotated.bam_readcount.vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#gatherer>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#gatherer/all_files> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#gatherer/output_dir> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#gatherer/gathered_files> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/gatherer.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_readgroups>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#tumor_bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_index/indexed_vcf> ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#tumor_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#normal_bam>
        cwl:inputBinding    [ CommandLineBinding:position  3 ;
                              CommandLineBinding:prefix    "-I:normal"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_min_var_freq>
        cwl:default  1e-01 ;
        sld:type     xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#select_variants/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#target_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/artifact_detection_mode>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#artifact_detection_mode> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#dbsnp_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_ensembl_version>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_ensembl_version> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_to_table_fields>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_to_table_fields> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/mills>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#mills> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_gnomADe_allele_freq.cwl#filtered_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "annotated.af_filtered.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/verify_bam_id.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--vcf" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--vcf" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_somatic_llr/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_depth/depth_filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/min_var_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#min_var_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#region_filter/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#roi_bed>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#filter_docm_variants>
        cwl:default  true ;
        sld:type     xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_verify_bam_id_depth>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/verify_bam_id_depth> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/synonyms_file>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#synonyms_file> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#annotate_coding_only>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#readgroups>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_antitarget_coverage>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/normal_antitarget_coverage> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bqsr.cwl#bqsr_table>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "bqsr.table" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "bqsr.table" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#intervals_target>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/intervals_target> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#min_mapping_quality>
        cwl:default       0 ;
        cwl:inputBinding  [ CommandLineBinding:position
                          -1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          -1 ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#bait_intervals>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--targets"
                          ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_insert_size_metrics.cwl#insert_size_histogram>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_depth.cwl#depth_filtered_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "depth_filtered.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/max_alt_alleles_in_normal_count>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#max_alt_alleles_in_normal_count> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#minimum_base_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_target_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#p_value>
        cwl:default       9.9e-01 ;
        cwl:inputBinding  [ CommandLineBinding:position
                          7 ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#method>
        cwl:default       "hybrid" ;
        cwl:inputBinding  [ CommandLineBinding:position  6 ;
                            CommandLineBinding:prefix    "--method"
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/unfiltered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#dbsnp_vcf>
        cwl:inputBinding    [ CommandLineBinding:position  5 ;
                              CommandLineBinding:prefix    "--dbsnp"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf/data_type> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf/sample_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf/snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf/indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf/annotated_bam_readcount_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#minimum_base_quality>
        cwl:default       1 ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_BASE_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_BASE_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_BASE_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_BASE_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_BASE_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_BASE_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_BASE_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_BASE_QUALITY=" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/bqsr_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#bqsr_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#index>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#index/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#index/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mutect_max_alt_allele_in_normal_fraction>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mutect_max_alt_allele_in_normal_fraction> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#reference_fasta>
        cwl:inputBinding  [ CommandLineBinding:position
                          -5 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          -5 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/align_and_tag.cwl#aligned_bam>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "refAlign.bam" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "refAlign.bam" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_cache_dir>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_cache_dir> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#reindex/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#call_regions>
        rdfs:comment        "bgzip-compressed, tabix-indexed BED file specifiying regions to which variant analysis will be restricted" ;
        cwl:inputBinding    [ CommandLineBinding:position  -5 ;
                              CommandLineBinding:prefix    "--callRegions"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#sample_name>
        cwl:default       "TUMOR" ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--sample"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--sample"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--sample"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--sample"
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#germline>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.Germline.vcf" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.Germline.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_alignment_summary_metrics.cwl#metric_accumulation_level>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_summary>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_summary> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_max_alt_alleles_in_normal_count>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#output_vcf_basename>
        cwl:default  "fpfilter" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl#strelka_vcf>
        cwl:inputBinding    [ CommandLineBinding:position  4 ;
                              CommandLineBinding:prefix    "--variant:strelka"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#bqsr_intervals>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#reference_coverage>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/reference_coverage> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_max_alt_allele_in_normal_fraction>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_bam_to_cram/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_bams_samtools.cwl#name>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_gnomADe_allele_freq.cwl#maximum_population_allele_frequency>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            cwl:valueFrom                "${\n    return [\n        \"--filter\",\n        [\n            \"gnomADe_AF\", \"<\", inputs.maximum_population_allele_frequency,\n            \"or not\", \"gnomADe_AF\"\n        ].join(\" \")\n    ]\n}\n"
                          ] ;
        sld:type          xsd:float .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#sample_name>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#do_cle_vcf_filter>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/bait_intervals>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#summary_intervals> ;
        cwl:valueFrom  "$(self.file)" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_cram>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_index_cram/indexed_cram> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#summary_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/target_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#target_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id/verify_bam_id_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_indel_bam_readcount_tsv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/indel_bam_readcount_tsv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#per_target_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/variants>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/snvs> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/known_indels>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#known_indels> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#annotated_bam_readcount_vcf>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/annotated_bam_readcount_vcf> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bgzip.cwl#file>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#per_base_coverage_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
        sld:type           sld:null , cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#normal_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_pick>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_pick> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#cosmic_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/summary_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#summary_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf/annotated_bam_readcount_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#somatic_hc>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.Somatic.hc.vcf" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.Somatic.hc.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#hgvs_annotation>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#tumor_antitarget_coverage>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.tumor_bam.nameroot).antitargetcoverage.cnn" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_docm.cwl#tumor_bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          -2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/min_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#readcount_minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#region_file>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-j" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/max_alt_allele_in_normal_fraction>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_max_alt_allele_in_normal_fraction> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_cle/filter>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#do_cle_vcf_filter> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#add_gt>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#add_gt/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#add_gt/processed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_strelka_gt.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#bam>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#somalier_concordance_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance/somalier_pairs> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/align_and_tag.cwl#bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_target_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/call_regions>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta_call_regions> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_bam.cwl#bam>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#somatic>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.Somatic.vcf" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.Somatic.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#tumor_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/reference_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_verify_bam_id_depth>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/verify_bam_id_depth> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_mapq0.cwl#threshold>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          xsd:float .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#indel_bam_readcount_tsv>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sample)_bam_readcount_indel.tsv" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sample)_bam_readcount_indel.tsv" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_base_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/per_base_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta_non_wgs>
        cwl:default  true ;
        sld:type     xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/strand_filter>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#strand_filter> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_mapq0/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#index>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#index/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#index/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#verify_bam_id_depth>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/verify_bam_id_depth> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#ensembl_species>
        rdfs:comment      "ensembl species - Must be present in the cache directory. Examples: 'homo_sapiens' or 'mus_musculus'" ;
        cwl:inputBinding  [ CommandLineBinding:position  13 ;
                            CommandLineBinding:prefix    "--species"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#variants_to_table_genotype_fields>
        cwl:default  "AD" , "GT" ;
        sld:type     [ sld:items  xsd:string ;
                       sld:type   sld:array
                     ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_antitarget_coverage>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/tumor_antitarget_coverage> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_index_cram>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_index_cram/cram> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_index_cram/indexed_cram> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_cram.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#final_filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_index/indexed_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#apply_bqsr/bqsr_table>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr/bqsr_table> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_p_value>
        cwl:default  9.9e-01 ;
        sld:type     xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#normal_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/sample_name>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#sample_name> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka_filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/pindel_insert_size>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#pindel_insert_size> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#dbsnp_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_plugins>
        cwl:default  "Wildtype" , "Downstream" ;
        sld:type     sld:null ;
        sld:type     [ sld:items  xsd:string ;
                       sld:type   sld:array
                     ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#min_var_freq>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#max_alt_allele_in_normal_fraction>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_verify_bam_id_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/verify_bam_id_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#pick>
        cwl:default       "flag_pick" ;
        cwl:inputBinding  [ CommandLineBinding:position  7 ;
                            CommandLineBinding:prefix    "--" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          sld:null ;
        sld:type          [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#pick/flag_pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#pick/flag_pick_allele> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#pick/flag_pick_allele_gene> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#pick/per_gene> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#pick/pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#pick/pick_allele> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#pick/pick_allele_gene> ;
                            sld:type     sld:enum
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_cache_dir>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_cache_dir> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/max_normal_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_max_normal_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/filter_mapq0_threshold>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_mapq0_threshold> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/cosmic_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#cosmic_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align/readgroup>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#readgroups> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bam_to_cram>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bam_to_cram/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bam_to_cram/bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bam_to_cram/cram> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_to_cram.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#intervals_antitarget>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/intervals_antitarget> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/name_sort.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "sort BAM by name" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-t"
                                   [ cwl:valueFrom  "$(runtime.cores)" ]
                                   "-m" "12G" "-n" "-o"
                                   [ cwl:valueFrom  "$(inputs.bam.nameroot).NameSorted.bam" ]
                                 ) ;
        cwl:arguments            ( "-t"
                                   [ cwl:valueFrom  "$(runtime.cores)" ]
                                   "-m" "12G" "-n" "-o"
                                   [ cwl:valueFrom  "$(inputs.bam.nameroot).NameSorted.bam" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/sambamba" "sort" ) ;
        cwl:baseCommand          ( "/usr/bin/sambamba" "sort" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/name_sort.cwl#bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/name_sort.cwl#name_sorted_bam> ;
        cwl:requirements         [ a                             cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin  8 ;
                                   ResourceRequirement:ramMin    16000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/sambamba-cwl:0.6.4"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/sambamba-cwl:0.6.4"
                                 ] ;
        cwl:requirements         [ a                             cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin  8 ;
                                   ResourceRequirement:ramMin    16000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#chromosome>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-c" ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#bams>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#cat>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#cat/pindel_outs> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#cat/pindel_out> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cat_out.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_cram>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_index_cram/indexed_cram> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#vcf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/hs_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_hc_snvs/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/somatic_hc_snvs> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_indels/filtered_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_hc_indels/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_gnomADe_maximum_population_allele_frequency>
        sld:type  xsd:float .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/dbsnp_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#dbsnp_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_ensembl_version>
        rdfs:comment  "ensembl version - Must be present in the cache directory. Example: 95" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel_somatic_filter.cwl#pindel_output_summary>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/pindel_insert_size>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#pindel_insert_size> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/metric_accumulation_level>
        cwl:valueFrom  "ALL_READS" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#merge/bams>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align/tagged_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/cle_vcf_filter>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#cle_vcf_filter> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/picard_metric_accumulation_level>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#picard_metric_accumulation_level> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#tumor_target_coverage>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.tumor_bam.nameroot).targetcoverage.cnn" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#max_alt_allele_in_normal_fraction>
        cwl:inputBinding  [ CommandLineBinding:position  10 ;
                            CommandLineBinding:prefix    "--max_alt_allele_in_normal_fraction"
                          ] ;
        sld:type          xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/strand_filter>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#strand_filter> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_indel_bam_readcount_tsv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/normal_indel_bam_readcount_tsv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#snvs>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/snvs> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine/pindel_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#vcf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_indels>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_indels/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_indels/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_ensembl_version>
        rdfs:comment  "ensembl version - Must be present in the cache directory. Example: 95" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#final_tsv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_vep_fields_to_table/annotated_variants_tsv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/min_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/reference_fasta> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/min_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/sample> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/indel_bam_readcount_tsv> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Unaligned BAM to BQSR and VCF" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mark_duplicates_and_sort> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#name_sort> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#merge> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#apply_bqsr> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#index_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#known_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bams> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mills> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#readgroups> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#final_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#final_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mark_duplicates_metrics_file> ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#index>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#index/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#index/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#bqsr_intervals>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#tumor_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#picard_metric_accumulation_level>
        cwl:default  "ALL_READS" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#minimum_base_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#insertions>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "all_SI" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bqsr.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:position  3 ;
                              CommandLineBinding:prefix    "-I"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  3 ;
                              CommandLineBinding:prefix    "-I"
                            ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index_snvs>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index_snvs/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index_snvs/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/align_and_tag.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#synonyms_file>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "--synonyms"
                          ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/metric_accumulation_level> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/alignment_summary_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_alignment_summary_metrics.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl#docm_vcf>
        cwl:inputBinding    [ CommandLineBinding:position  4 ;
                              CommandLineBinding:prefix    "--alleles"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table/fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table/genotype_fields> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table/variants_tsv> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/variants_to_table.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/picard_metric_accumulation_level>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#picard_metric_accumulation_level> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_cle.cwl#cle_filtered_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "annotated_filtered.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#decompose/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_docm_variants/merged_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_docm.cwl#filter_docm_variants>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "${\n  if(inputs.filter_docm_variants){\n    return \"1\";\n  } else {\n    return \"0\";\n  }\n}\n"
                          ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/split_interval_list.cwl#interval_list>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "INPUT=" ;
                            CommandLineBinding:separate  false
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/panel_of_normals_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#panel_of_normals_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_min_coverage>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_min_coverage> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/final_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/readgroups> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/mills> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/known_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/bqsr_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/bams> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/final_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/mark_duplicates_metrics_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka_cpu_reserved>
        cwl:default  8 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/coding_only>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_coding_only> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#loh_hc_snvs>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/loh_hc> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_max_normal_freq>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_to_table_fields>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_to_table_fields> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_target_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/per_target_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/docm_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/filter_docm_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/docm_variants_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/insert_size>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#insert_size> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_min_coverage>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_min_coverage> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_somatic_llr>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_somatic_llr/threshold> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_somatic_llr/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_somatic_llr/somatic_llr_filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_somatic_llr.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl#somalier_pairs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "concordance.somalier.pairs.tsv" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_insert_size_metrics.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "collect insert size metrics" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeMetrics.txt" ]
                                   "H="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ]
                                 ) ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeMetrics.txt" ]
                                   "H="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_insert_size_metrics.cwl#metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_insert_size_metrics.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_insert_size_metrics.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_insert_size_metrics.cwl#insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_insert_size_metrics.cwl#insert_size_histogram> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  18000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  18000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_add_variants.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "CombineVariants (GATK 3.6)" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-genotypeMergeOptions" "PRIORITIZE" "--rod_priority_list" "callers,docm" "--setKey" "null" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/merged.vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_add_variants.cwl#docm_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_add_variants.cwl#callers_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_add_variants.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_add_variants.cwl#merged_vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     9000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#bait_intervals>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "mutect parallel workflow" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#merge> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#index> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#split_interval_list> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#max_alt_alleles_in_normal_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#cosmic_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#max_alt_allele_in_normal_fraction> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#artifact_detection_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#scatter_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#panel_of_normals_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#tumor_bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#unfiltered_vcf> ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:MultipleInputFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl#pindel_vcf>
        cwl:inputBinding    [ CommandLineBinding:position  5 ;
                              CommandLineBinding:prefix    "--variant:pindel"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#min_coverage>
        cwl:default  8 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/output_contigs>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta_output_contigs> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#variants>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(runtime.outdir)/$(self.basename)"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            cwl:valueFrom                "$(runtime.outdir)/$(self.basename)"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/synonyms_file> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/somalier_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/variants_to_table_genotype_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mills> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_ensembl_assembly> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mutect_max_alt_allele_in_normal_fraction> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/hgvs_annotation> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_max_normal_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/pindel_insert_size> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_readgroups> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/omni_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_bams> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/annotate_coding_only> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_cache_dir> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/strelka_cpu_reserved> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mutect_scatter_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_cram_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/picard_metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_ensembl_version> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/cosmic_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_bams> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/docm_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/per_base_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_readgroups> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mutect_max_alt_alleles_in_normal_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/qc_minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/cle_vcf_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_min_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_p_value> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/bqsr_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_cram_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_to_table_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_ensembl_species> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/summary_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_strand_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/variants_to_table_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mutect_artifact_detection_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/qc_minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/per_target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/panel_of_normals_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/known_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/custom_gnomad_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/target_intervals> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_summary_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/pindel_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/final_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_cram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/final_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/pindel_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_flagstats> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_summary> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/somalier_concordance_statistics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_mark_duplicates_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_verify_bam_id_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mutect_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_flagstats> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_cram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_mark_duplicates_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/somalier_concordance_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_alignment_summary_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_summary_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/strelka_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_alignment_summary_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/docm_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_per_target_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_verify_bam_id_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mutect_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/strelka_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/final_filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#diagram>
        cwl:inputBinding  [ CommandLineBinding:position  7 ;
                            CommandLineBinding:prefix    "--diagram"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_min_var_freq>
        cwl:default  5e-02 ;
        sld:type     xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bam_to_cram/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter/filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index_indels/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_indels/merged_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#bgzip/file>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_cle.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "cle_annotated_vcf_filter" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "$(inputs.vcf.path)" "$(runtime.outdir)" ) ;
        cwl:baseCommand          ( "/usr/bin/perl" "/usr/bin/docm_and_coding_indel_selection.pl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_cle.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_cle.cwl#filter> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_cle.cwl#cle_filtered_vcf> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#normal_bam>
        cwl:inputBinding    [ CommandLineBinding:position
                          2 ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/reference_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#minimum_mapping_quality>
        cwl:default       1 ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_MAPPING_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_MAPPING_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_MAPPING_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_MAPPING_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_MAPPING_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_MAPPING_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_MAPPING_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_MAPPING_QUALITY=" ] ;
        sld:type          sld:null , xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#insert_size>
        cwl:default  400 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#custom_clinvar_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl#bam_2>
        cwl:inputBinding    [ CommandLineBinding:position
                          4 ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#final_name>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#bait_intervals>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter/variant_caller>
        cwl:valueFrom  "pindel" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_alignment_summary_metrics.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "collect alignment summary metrics" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "OUTPUT="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ]
                                 ) ;
        cwl:arguments            ( "OUTPUT="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_alignment_summary_metrics.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_alignment_summary_metrics.cwl#metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_alignment_summary_metrics.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_alignment_summary_metrics.cwl#alignment_summary_metrics> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  18000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  18000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf/data_type> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf/sample_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf/indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf/snv_bam_readcount_tsv> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf/annotated_bam_readcount_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#summary_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/min_coverage>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_min_coverage> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  8 ;
                            CommandLineBinding:prefix    "--fasta"
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/gatherer.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-t" ) ;
        cwl:baseCommand          ( "/bin/cp" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/gatherer.cwl#output_dir> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/gatherer.cwl#all_files> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/gatherer.cwl#gathered_files> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "ubuntu:xenial"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/per_target_coverage>
        cwl:default  false .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#mills>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#minimum_base_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_somatic_llr.cwl#threshold>
        cwl:inputBinding  [ CommandLineBinding:position  -2 ;
                            CommandLineBinding:prefix    "--llr-threshold"
                          ] ;
        sld:type          xsd:float .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mutect_artifact_detection_mode>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#qc_minimum_base_quality>
        cwl:default  0 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/qc_minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#qc_minimum_base_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#region_filter/filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#max_normal_freq>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_cram.cwl#cram>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_coding_only>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#germline_snvs>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/germline> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#custom_gnomad_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#select_variants/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#index/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_variants_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#index2/indexed_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/omni_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#omni_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#strelka_unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/strelka_unfiltered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/dbsnp_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#dbsnp_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/per_base_coverage>
        cwl:default  false .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#region_filter/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--fasta"
                          ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#somatic_variants>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/somatic_variants> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_gnomADe_maximum_population_allele_frequency>
        cwl:default  1e-03 ;
        sld:type     xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter/filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/gatherer.cwl#all_files>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl#somalier_samples>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "concordance.somalier.samples.tsv" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#process>
        cwl:in       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#process/vcf> ;
        cwl:out      <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#process/processed_vcf> ;
        cwl:run      <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl> ;
        cwl:scatter  ( <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#process/vcf> ) .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_strand_filter>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_strand_filter> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#drop_low_coverage>
        cwl:inputBinding  [ CommandLineBinding:position  10 ;
                            CommandLineBinding:prefix    "--drop-low-coverage"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_base_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/per_base_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/final_name>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#final_name> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#indels>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "results/variants/somatic.indels.vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_base_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mutect_max_alt_alleles_in_normal_count>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_add_variants.cwl#merged_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "merged.vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_to_cram.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-T"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-T"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_docm_variants/callers_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine/combined_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_indels/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_indels/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/custom_gnomad_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#custom_gnomad_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_mapq0.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "filter vcf for variants with high percentage of mapq0 reads" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "/bin/bash" "/usr/bin/mapq0_vcf_filter.sh"
                                   [ cwl:valueFrom  "$(runtime.outdir)/mapq_filtered.vcf.gz" ]
                                 ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_mapq0.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_mapq0.cwl#tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_mapq0.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_mapq0.cwl#threshold> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_mapq0.cwl#mapq0_filtered_vcf> ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     8000 ;
                                   ResourceRequirement:tmpdirMin  10000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/mapq0-filter:v0.3"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_filter>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_filter/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_filter/docm_raw_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_filter/filter_docm_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_filter/normal_bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_filter/docm_filtered_variants> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_docm.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#index>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#index/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#index/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/intervals_to_bed.cwl#interval_bed>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "interval_list.bed" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#index>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#index/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#index/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "add bam_readcount info to vcf" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "vcf-readcount-annotator" ) ;
        cwl:baseCommand          ( "vcf-readcount-annotator" ) ;
        cwl:baseCommand          ( "vcf-readcount-annotator" ) ;
        cwl:baseCommand          ( "vcf-readcount-annotator" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#data_type> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#variant_type> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#sample_name> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#annotated_bam_readcount_vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "griffithlab/vatools:3.1.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "griffithlab/vatools:3.1.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "griffithlab/vatools:3.1.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "griffithlab/vatools:3.1.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_base_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_base_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#docm_filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/docm_filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_bgzip>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_bgzip/file> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_bgzip/bgzipped_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bgzip.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#apply_bqsr/output_name>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#final_name> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bams>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_bams> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/max_normal_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#max_normal_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/hs_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/filter_gnomADe_maximum_population_allele_frequency>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_gnomADe_maximum_population_allele_frequency> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/cle_vcf_filter>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cle_vcf_filter> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#gatherer/output_dir>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#output_dir> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#normal_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:position
                          -4 ] ;
        cwl:inputBinding    [ CommandLineBinding:position
                          -4 ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#germline_hc_snvs>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/germline_hc> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#decompose_index/indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#cn_scatter_plot>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.tumor_bam.nameroot)-scatter.pdf" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/pick>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_pick> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#align/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bams> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#filter_docm_variants>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/variants_to_table.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "SelectVariants (GATK 3.6)" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "--allowMissingData" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/variants.tsv" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantsToTable" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/variants_to_table.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/variants_to_table.cwl#genotype_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/variants_to_table.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/variants_to_table.cwl#fields> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/variants_to_table.cwl#variants_tsv> ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/final_name>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_name> ;
        cwl:valueFrom  "$(self).bam" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_to_table_fields>
        cwl:default  "HGVSp" , "HGVSc" ;
        sld:type     [ sld:items  xsd:string ;
                       sld:type   sld:array
                     ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#final_filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/final_filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter/unfiltered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "varscan v2.4.2 somatic" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/usr/bin/varscan_helper.sh" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#strand_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#roi_bed> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#min_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#p_value> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#tumor_bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#snvs> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  12000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/plugins>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_plugins> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_pick>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_pick> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#minimum_mapping_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#get_chromosome_list/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cat_all.cwl#all_chromosome_pindel_head>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "all_chromosome_pindel.head" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#cpu_reserved>
        cwl:default  8 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index_indels>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index_indels/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#index_indels/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_to_table_fields>
        cwl:default  "HGVSp" , "HGVSc" ;
        sld:type     [ sld:items  xsd:string ;
                       sld:type   sld:array
                     ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#deletions>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "all_D" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#bait_intervals>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf/annotated_bam_readcount_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/docm_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/target_intervals>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_target_intervals> ;
        cwl:valueFrom  "$(self.file)" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/max_normal_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/variants> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/germline> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/loh> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/somatic> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/loh_hc> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/somatic_hc> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/germline_hc> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#index_bam/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#apply_bqsr/bqsr_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka_exome_mode>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_docm.cwl#docm_filtered_variants>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "docm_filtered_variants.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance/bam_1>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/mills>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mills> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bams>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf/data_type>
        cwl:default  "DNA" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_mark_duplicates_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/mark_duplicates_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#per_base_coverage>
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_BASE_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_BASE_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_BASE_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_BASE_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_BASE_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_BASE_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_BASE_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_BASE_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Apply filters to VCF file" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_somatic_llr> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_cle> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_gnomADe_allele_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_mapq0> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#do_cle_vcf_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_gnomADe_maximum_population_allele_frequency> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#sample_names> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_minimum_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_somatic_llr_threshold> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_mapq0_threshold> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filtered_vcf> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl#interval_list>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/set_filter_status.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#cat_all/chromosome_pindel_outs>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/per_chromosome_pindel_out> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#decompose>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#decompose/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#decompose/decomposed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vt_decompose.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#per_base_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_target_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/per_target_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/hs_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_docm.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Filter variants from the DoCM detector" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "$(runtime.outdir)/docm_filtered_variants.vcf" ) ;
        cwl:baseCommand          ( "/usr/bin/perl" "/usr/bin/docm_filter.pl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_docm.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_docm.cwl#filter_docm_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_docm.cwl#docm_raw_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_docm.cwl#tumor_bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_docm.cwl#docm_filtered_variants> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.4.1"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_target_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/bqsr_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#bqsr_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_summary_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/alignment_summary_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#loh_indels>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/loh> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#normal_readgroups>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_bams>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#normal_bams> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#add_gt/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_indels/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#reindex>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#reindex/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#reindex/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge/vcfs> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge/merged_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#synonyms_file>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "varscan somatic workflow" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#p_value> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#max_normal_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#roi_bed> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#strand_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#min_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#tumor_bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#germline_hc_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#loh_hc_snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#germline_hc_snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#loh_snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#germline_snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic_snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#germline_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#loh_hc_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic_hc_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#loh_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic_hc_snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic_indels> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_mapq0/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Detect Docm variants" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#decompose> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#bgzip2> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#bgzip> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#index> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#index2> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#filter_docm_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#interval_list> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_variants_vcf> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_mapq0.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/insert_size> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/tumor_bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/unfiltered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_mapq0.cwl#tumor_bam>
        cwl:inputBinding    [ CommandLineBinding:position
                          2 ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/get_chromosome_list.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "bash" "-c" "/bin/grep -v '^@' $1 | /usr/bin/cut -f 1 | /usr/bin/sort | grep -v ^$ | /usr/bin/uniq" "--" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/get_chromosome_list.cwl#interval_list> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/get_chromosome_list.cwl#chromosome_list> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "ubuntu:xenial"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "chromosome.list" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#loh_snvs>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_snvs/loh> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#bgzip/bgzipped_file> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/qc_minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#qc_minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_ensembl_version>
        rdfs:comment  "ensembl version - Must be present in the cache directory. Example: 95" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#loh_hc_indels>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/loh_hc> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_cram.cwl#indexed_cram>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.cram.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.cram.basename)" ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine/varscan_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#access>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--access"
                          ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/artifact_detection_mode>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_artifact_detection_mode> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/filter_docm_variants>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_docm_variants> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#normal_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_gnomADe_allele_freq/maximum_population_allele_frequency>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_gnomADe_maximum_population_allele_frequency> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#pindel_insert_size>
        cwl:default  400 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#strelka_cpu_reserved>
        cwl:default  8 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#tumor_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "HaplotypeCaller (GATK 3.6)" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-gt_mode" "GENOTYPE_GIVEN_ALLELES" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/docm_raw_variants.vcf" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "HaplotypeCaller" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl#docm_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl#interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl#normal_bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl#docm_raw_variants> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  9000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#coding_only>
        cwl:default       false ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--coding_only"
                          ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/normalize_variants.cwl#normalized_vcf>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "normalized.vcf.gz" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "normalized.vcf.gz" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "normalized.vcf.gz" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "normalized.vcf.gz" ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics>
        cwl:in             <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/per_base_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/per_target_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/output_prefix> ;
        cwl:out            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/hs_metrics> ;
        cwl:run            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/bait_intervals> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/target_intervals> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/output_prefix> ) ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/bait_intervals> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/target_intervals> <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/output_prefix> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/cache_dir>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_cache_dir> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#merge/name>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#final_name> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#merge/vcfs>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#process/processed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_artifact_detection_mode>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#samtools_flagstat>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#samtools_flagstat/bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#samtools_flagstat/flagstats> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/samtools_flagstat.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_min_coverage>
        cwl:default  8 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#indexed_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#index/indexed_vcf> ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#p_value>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cosmic_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_readgroups>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#normal_readgroups> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#merge/vcfs>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#long_insertions>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "all_LI" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vt_decompose.cwl#decomposed_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "decomposed.vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "decomposed.vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "decomposed.vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "decomposed.vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "decomposed.vcf.gz" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "decomposed.vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#final_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/final_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#tandems>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "all_TD" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#insert_size_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/insert_size_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_bams>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#panel_of_normals_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bqsr_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#bqsr_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/per_target_coverage>
        cwl:default  false .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#apply_bqsr/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_gatk_haplotype_caller.cwl#docm_raw_variants>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "docm_raw_variants.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#dbsnp_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#region_filter/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_index_cram/cram>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bam_to_cram/cram> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mark_duplicates_and_sort.cwl#output_name>
        cwl:default       "MarkedSorted.bam" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/verify_bam_id.cwl#verify_bam_id_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).VerifyBamId.selfSM" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).VerifyBamId.selfSM" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#scatter_count>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_filter/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_depth/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_cle/cle_filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#remove_end_tags/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#region_filter/filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/mutect_artifact_detection_mode>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_artifact_detection_mode> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#reference_coverage>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "reference.cnn" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cn_diagram>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/cn_diagram> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_depth/sample_names>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#sample_names> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#bait_intervals>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "BAIT_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "BAIT_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "BAIT_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "BAIT_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "BAIT_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "BAIT_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "BAIT_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "BAIT_INTERVALS=" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_cram_name>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#normal_cram_name> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_bgzip/file>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#indel_bam_readcount_tsv>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_somatic_llr/threshold>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_somatic_llr_threshold> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#bgzip>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#bgzip/file> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#bgzip/bgzipped_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bgzip.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#bgzip>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#bgzip/file> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#bgzip/bgzipped_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bgzip.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#snv_bam_readcount_tsv>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#custom_clinvar_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/per_target_coverage>
        cwl:default  false .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#hard_filter/exclude_filtered>
        cwl:default  true .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#cosmic_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_somatic_llr.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "use the binomial/llr somatic filter to weed out low confidence variants" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "--overwrite"
                                   [ cwl:valueFrom  "$(runtime.outdir)/somatic_llr_filtered.vcf" ]
                                 ) ;
        cwl:baseCommand          ( "/opt/conda/bin/python3" "/usr/bin/somatic_llr_filter.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_somatic_llr.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_somatic_llr.cwl#threshold> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_somatic_llr.cwl#somatic_llr_filtered_vcf> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/somatic-llr-filter:v0.4.1"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/cosmic_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#cosmic_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/p_value>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_p_value> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_hc_indels/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/somatic_hc_indels> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#filter_docm_variants>
        cwl:default  true ;
        sld:type     xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "bgzip and index VCF" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#bgzip> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#index> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#indexed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#somaticfilter/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#index/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#bgzip/bgzipped_file> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#annotate_coding_only>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#vcf>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/set_filter_status.cwl#vcf>
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/intervals_to_bed.cwl#interval_list>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#get_chromosome_list>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#get_chromosome_list/interval_list> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#get_chromosome_list/chromosome_list> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/get_chromosome_list.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#bqsr_intervals>
        sld:type  sld:null ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/summary_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#summary_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_base_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_scatter_count>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vt_decompose.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "run vt decompose" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-s" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/decomposed.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-s" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/decomposed.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-s" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/decomposed.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-s" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/decomposed.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-s" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/decomposed.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-s" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/decomposed.vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "vt" "decompose" ) ;
        cwl:baseCommand          ( "vt" "decompose" ) ;
        cwl:baseCommand          ( "vt" "decompose" ) ;
        cwl:baseCommand          ( "vt" "decompose" ) ;
        cwl:baseCommand          ( "vt" "decompose" ) ;
        cwl:baseCommand          ( "vt" "decompose" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vt_decompose.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vt_decompose.cwl#decomposed_vcf> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "quay.io/biocontainers/vt:0.57721--hf74b74d_1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "quay.io/biocontainers/vt:0.57721--hf74b74d_1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "quay.io/biocontainers/vt:0.57721--hf74b74d_1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "quay.io/biocontainers/vt:0.57721--hf74b74d_1"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "quay.io/biocontainers/vt:0.57721--hf74b74d_1"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "quay.io/biocontainers/vt:0.57721--hf74b74d_1"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_vcf.cwl#merged_vcf_basename>
        cwl:default  "merged" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_cache_dir>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_base_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#per_base_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#indels>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/indels> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/variants_to_table.cwl#genotype_fields>
        cwl:default       "AD" , "AF" , "DP" , "GT" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          [ cwl:inputBinding  [ CommandLineBinding:prefix
                                              "-GF" ] ;
                            sld:items         xsd:string ;
                            sld:type          sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl#exclude_filtered>
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--excludeFiltered"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--excludeFiltered"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--excludeFiltered"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--excludeFiltered"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--excludeFiltered"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--excludeFiltered"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--excludeFiltered"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--excludeFiltered"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#reference_cnn>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-r" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_strand_filter>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_strand_filter> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/output_prefix>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_target_intervals> ;
        cwl:valueFrom  "target-$(self.label)" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_pick>
        sld:type  sld:null ;
        sld:type  [ sld:symbols  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_pick/flag_pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_pick/flag_pick_allele> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_pick/flag_pick_allele_gene> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_pick/per_gene> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_pick/pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_pick/pick_allele> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_pick/pick_allele_gene> ;
                    sld:type     sld:enum
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/picard_metric_accumulation_level>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#picard_metric_accumulation_level> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_index>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_index/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_index/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/filter_somatic_llr_threshold> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/filter_minimum_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/filter_mapq0_threshold> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/sample_names> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/do_cle_vcf_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/filter_gnomADe_maximum_population_allele_frequency> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/variants_to_table_genotype_fields>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#variants_to_table_genotype_fields> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#ensembl_assembly>
        rdfs:comment      "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ;
        cwl:inputBinding  [ CommandLineBinding:position  11 ;
                            CommandLineBinding:prefix    "--assembly"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#min_var_freq>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#target_intervals>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/annotated_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl#mutect_vcf>
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant:mutect"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_add_variants.cwl#docm_vcf>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--variant:docm"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/omni_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#omni_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_mapq0/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_gnomADe_allele_freq/filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/usr/bin/python" "/usr/local/bin/cnvkit.py" "batch" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#male_reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#drop_low_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#scatter_plot> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#reference_cnn> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#access> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#method> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#diagram> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#reference_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#tumor_segmented_ratios> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#tumor_target_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#cn_diagram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#normal_antitarget_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#tumor_bin_level_ratios> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#tumor_antitarget_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#cn_scatter_plot> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#normal_target_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#intervals_antitarget> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#intervals_target> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "etal/cnvkit:0.9.5"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:ramMin     4000 ;
                                   ResourceRequirement:tmpdirMin  10000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "process VCF workflow" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#bgzip> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#index> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#add_gt> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#processed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/qc_minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#qc_minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/metric_accumulation_level>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#picard_metric_accumulation_level> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#align_and_tag/readgroup>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#readgroup> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mutect.cwl#interval_list>
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/p_value> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/max_normal_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/min_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/strand_filter> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/chromosome>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#get_chromosome_list/chromosome_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/apply_bqsr.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "-I"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "-I"
                            ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#per_target_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/sample_name>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#sample_name> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_per_base_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_base_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#interval_list>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_depth.cwl#minimum_depth>
        cwl:inputBinding  [ CommandLineBinding:position  -3 ;
                            CommandLineBinding:prefix    "--minimum_depth"
                          ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_target_coverage>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/tumor_target_coverage> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_ensembl_assembly>
        rdfs:comment  "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Exome QC workflow" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#select_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#samtools_flagstat> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#summary_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#omni_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_base_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#picard_metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#minimum_base_quality> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_target_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#alignment_summary_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#summary_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#flagstats> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#insert_size_histogram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#per_target_coverage_metrics> ;
        cwl:requirements         [ a                           cwl:SchemaDefRequirement ;
                                   SchemaDefRequirement:types  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file>
                                 ] ;
        cwl:requirements         [ a                           cwl:SchemaDefRequirement ;
                                   SchemaDefRequirement:types  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file>
                                 ] ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#normal_bam>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#known_indels>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#minimum_base_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#tumor_bam>
        cwl:inputBinding    [ CommandLineBinding:position  -3 ;
                              CommandLineBinding:prefix    "--tumorBam"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_vep_fields_to_table.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "add VEP annotation to report" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ]
                                 ) ;
        cwl:baseCommand          ( "vep-annotation-reporter" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_vep_fields_to_table.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_vep_fields_to_table.cwl#tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_vep_fields_to_table.cwl#prefix> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_vep_fields_to_table.cwl#vep_fields> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_vep_fields_to_table.cwl#annotated_variants_tsv> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "griffithlab/vatools:3.1.0"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/vep_ensembl_species>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#vep_ensembl_species> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/intervals_to_bed.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/usr/bin/perl" "/usr/bin/intervals_to_bed.pl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/intervals_to_bed.cwl#interval_list> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/intervals_to_bed.cwl#interval_bed> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/perl_helper-cwl:1.0.0"
                                 ] ;
        cwl:stdout               "interval_list.bed" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#cn_diagram>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.tumor_bam.nameroot)-diagram.pdf" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_hc_indels>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_hc_indels/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#bgzip_and_index_hc_indels/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_add_variants.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#bam>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#normal_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id/bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id/verify_bam_id_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id/verify_bam_id_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/verify_bam_id.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#known_indels>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf/data_type>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_bam.cwl#indexed_bam>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.bam.basename)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.bam.basename)" ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#bgzip/file>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#add_gt/processed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_segmented_ratios>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/tumor_segmented_ratios> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_vep_fields_to_table.cwl#annotated_variants_tsv>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.prefix).annotated.tsv" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#process/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/snvs> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "False Positive filter" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ]
                                 ) ;
        cwl:arguments            ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ]
                                 ) ;
        cwl:arguments            ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ]
                                 ) ;
        cwl:arguments            ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ;
        cwl:baseCommand          ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ;
        cwl:baseCommand          ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ;
        cwl:baseCommand          ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#output_vcf_basename> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#sample_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#filtered_vcf> ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/fp_filter-cwl:1.0.1"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/fp_filter-cwl:1.0.1"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/fp_filter-cwl:1.0.1"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/fp_filter-cwl:1.0.1"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/roi_bed>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#roi_bed> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#docm_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#minimum_base_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter/unfiltered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#annotated_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "annotated.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#filter/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#intervals_target>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "${\n    var glob_base = \".target.bed\";\n    if (inputs.bait_intervals) {\n        glob_base = inputs.bait_intervals.nameroot + glob_base;\n    }\n    return glob_base;\n}\n" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/target_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#target_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mark_duplicates_and_sort.cwl#input_sort_order>
        cwl:default       "queryname" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          5 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_filter/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file/label>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_snvs>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_snvs/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_snvs/filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_snvs/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#merge_snvs/merged_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/set_filter_status.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cnvkit_batch.cwl#intervals_antitarget>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "${  \n    var glob_base = \".antitarget.bed\";\n    if (inputs.bait_intervals) {\n        glob_base = inputs.bait_intervals.nameroot + glob_base;\n    }   \n    return glob_base;\n}  \n" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#somaticfilter/pindel_output_summary>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#cat_all/all_chromosome_pindel_head> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_snv_bam_readcount_tsv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/normal_snv_bam_readcount_tsv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cat_out.cwl#pindel_outs>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_max_normal_freq>
        sld:type  xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/split_interval_list.cwl#split_interval_lists>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.interval_list" ] ;
        sld:type           [ sld:items  cwl:File ;
                             sld:type   sld:array
                           ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_index>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_index/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_index/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_mapq0>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_mapq0/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_mapq0/threshold> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_mapq0/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_mapq0/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_mapq0/mapq0_filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_mapq0.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf/data_type>
        cwl:default  "DNA" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/do_cle_vcf_filter>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#cle_vcf_filter> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_mapq0.cwl#mapq0_filtered_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "mapq_filtered.vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#target_intervals>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#strand_filter>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/known_indels>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#known_indels> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#alignment_summary_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/alignment_summary_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#strand_filter>
        cwl:default  0 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_docm_variants>
        cwl:default  true ;
        sld:type     xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_strelka_gt.cwl#vcf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_to_table_fields>
        cwl:default  "HGVSp" , "HGVSc" ;
        sld:type     sld:null ;
        sld:type     [ sld:items  xsd:string ;
                       sld:type   sld:array
                     ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#verify_bam_id/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#select_variants/filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_min_var_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_min_var_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka_unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/unfiltered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/normalize_variants.cwl#vcf>
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_alignment_summary_metrics.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "INPUT=" ] ;
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "INPUT=" ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#germline_hc_indels>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/germline_hc> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance/bam_2> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance/bam_1> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance/somalier_samples> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance/somalier_pairs> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/concordance.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_minimum_depth>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr_intervals>
        sld:type  sld:null ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm_filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/docm_variants_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/roi_bed> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/p_value> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/strand_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/min_coverage> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/snvs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/indels> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/exome_mode>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#exome_mode> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "pindel v0.2.5b8" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "/usr/bin/perl" "/usr/bin/pindel_helper.pl" "$(inputs.normal_bam.path)" "$(inputs.tumor_bam.path)" "$(inputs.insert_size)" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#region_file> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#insert_size> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#chromosome> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#tumor_bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#inversions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#insertions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#tandems> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#long_insertions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#deletions> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   4 ;
                                   ResourceRequirement:ramMin     64000 ;
                                   ResourceRequirement:tmpdirMin  100000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/min_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#readcount_minimum_base_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_bam.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "samtools index" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.bam.basename)" "$(runtime.outdir)/$(inputs.bam.basename).bai"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "cp" "$(inputs.bam.basename).bai" "$(runtime.outdir)/$(inputs.bam.nameroot).bai"
                                 ) ;
        cwl:arguments            ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.bam.basename)" "$(runtime.outdir)/$(inputs.bam.basename).bai"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "cp" "$(inputs.bam.basename).bai" "$(runtime.outdir)/$(inputs.bam.nameroot).bai"
                                 ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_bam.cwl#bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_bam.cwl#indexed_bam> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.bam)"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a            cwl:InitialWorkDirRequirement ;
                                   cwl:listing  "$(inputs.bam)"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bqsr_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#bqsr_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_per_target_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/per_target_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_per_base_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_base_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_min_var_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_min_var_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bqsr.cwl#known_sites>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            [ cwl:inputBinding  [ CommandLineBinding:position  4 ;
                                                  CommandLineBinding:prefix    "-knownSites"
                                                ] ;
                              sld:items         cwl:File ;
                              sld:type          sld:array
                            ] ;
        sld:type            [ cwl:inputBinding  [ CommandLineBinding:position  4 ;
                                                  CommandLineBinding:prefix    "-knownSites"
                                                ] ;
                              sld:items         cwl:File ;
                              sld:type          sld:array
                            ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/per_target_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/output_prefix> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/per_base_coverage> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/hs_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter/variant_caller> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter/unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter/filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/ensembl_species>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_ensembl_species> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/non_wgs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/output_contigs> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/call_regions> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/tumor_bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/diploid_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/small_candidates> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/somatic_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/all_candidates> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/tumor_only_variants> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/max_alt_alleles_in_normal_count>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_max_alt_alleles_in_normal_count> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#strelka/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/bait_intervals>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_base_intervals> ;
        cwl:valueFrom  "$(self.file)" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#min_var_freq>
        cwl:default  1e-01 ;
        sld:type     xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/summary_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#summary_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#custom_gnomad_vcf>
        cwl:inputBinding    [ CommandLineBinding:position  6 ;
                              cwl:valueFrom                "${\n    if (inputs.custom_gnomad_vcf) {\n        return ['--check_existing', '--custom', inputs.custom_gnomad_vcf.path + ',gnomADe,vcf,exact,0,AF,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH,AF_SAS']\n    }\n    else {\n        return []\n    }\n}\n"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/bams>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#bams> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/split_interval_list.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ cwl:valueFrom  "OUTPUT=$(runtime.outdir)" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/perl" "/usr/bin/split_interval_list_helper.pl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/split_interval_list.cwl#scatter_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/split_interval_list.cwl#interval_list> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/split_interval_list.cwl#split_interval_lists> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  6000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_bam_to_cram>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_bam_to_cram/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_bam_to_cram/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_bam_to_cram/cram> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_to_cram.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/sample>
        cwl:default  "NORMAL" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mark_duplicates_and_sort.cwl#metrics_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bait_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#bait_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#split_interval_list>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#split_interval_list/interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#split_interval_list/scatter_count> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#split_interval_list/split_interval_lists> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/split_interval_list.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/picard_metric_accumulation_level>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#picard_metric_accumulation_level> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_bams_samtools.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Samtools: merge" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "$(inputs.name).merged.bam" ) ;
        cwl:arguments            ( "$(inputs.name).merged.bam" ) ;
        cwl:baseCommand          ( "/opt/samtools/bin/samtools" "merge" ) ;
        cwl:baseCommand          ( "/opt/samtools/bin/samtools" "merge" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_bams_samtools.cwl#name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_bams_samtools.cwl#bams> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_bams_samtools.cwl#merged_bam> ;
        cwl:requirements         [ a                             cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin  4 ;
                                   ResourceRequirement:ramMin    8000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin  4 ;
                                   ResourceRequirement:ramMin    8000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Ensembl Variant Effect Predictor" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "--format" "vcf" "--vcf" "--fork" "4" "--term" "SO" "--transcript_version" "--offline" "--cache" "--symbol" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/annotated.vcf" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#ensembl_species> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#ensembl_assembly> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#custom_clinvar_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#synonyms_file> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#plugins> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#custom_gnomad_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#cache_dir> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#coding_only> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#everything> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#ensembl_version> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#vep_summary> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#annotated_vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/vep_helper-cwl:1.1.0"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   4 ;
                                   ResourceRequirement:ramMin     64000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#readgroups>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] ;
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/metric_accumulation_level>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#picard_metric_accumulation_level> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#concordance/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#somalier_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/min_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#readcount_minimum_base_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#loh>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.LOH.vcf" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.LOH.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_process_somatic.cwl#germline_hc>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.Germline.hc.vcf" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.Germline.hc.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#small_candidates>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/small_candidates> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#qc_minimum_mapping_quality>
        cwl:default  0 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_indel_bam_readcount_tsv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/tumor_indel_bam_readcount_tsv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_min_coverage>
        cwl:default  8 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#tumor_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bgzip_and_index.cwl#vcf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#decompose_variants>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#decompose_variants/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#decompose_variants/decomposed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vt_decompose.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_somatic_llr.cwl#somatic_llr_filtered_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "somatic_llr_filtered.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan/min_var_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_min_var_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_strand_filter>
        cwl:default  0 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/select_variants.cwl#interval_list>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/qc_minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#qc_minimum_base_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#tumor_readgroups>
        sld:type  [ sld:items  xsd:string ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/varscan_max_normal_freq>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#varscan_max_normal_freq> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_depth.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          -2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_per_target_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_target_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/min_coverage>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#min_coverage> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat>
        cwl:in       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/chromosome> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/insert_size> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/normal_bam> ;
        cwl:out      <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/per_chromosome_pindel_out> ;
        cwl:run      <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl> ;
        cwl:scatter  ( <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/chromosome> ) .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/remove_end_tags.cwl#vcf>
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#diploid_variants>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/diploid_variants> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bqsr.cwl#intervals>
        cwl:default       "chr18" , "chr9" , "chr12" , "chr2" , "chr19" , "chr8" , "chr5" , "chr14" , "chr4" , "chr15" , "chr22" , "chr1" , "chr10" , "chr17" , "chr16" , "chr11" , "chr6" , "chr7" , "chr21" , "chr20" , "chr13" , "chr3" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          [ cwl:inputBinding  [ CommandLineBinding:prefix
                                              "-L" ] ;
                            sld:items         xsd:string ;
                            sld:type          sld:array
                          ] ;
        sld:type          [ cwl:inputBinding  [ CommandLineBinding:prefix
                                              "-L" ] ;
                            sld:items         xsd:string ;
                            sld:type          sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#panel_of_normals_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment_summary_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/alignment_summary_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#varscan/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#normal_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mark_duplicates_and_sort/sorted_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#mutect/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#split_interval_list/split_interval_lists> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#index2/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#bgzip2/bgzipped_file> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf/filter_minimum_depth>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_minimum_depth> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#bait_intervals>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/exome_mode>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka_exome_mode> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Add snv and indel bam-readcount files to a vcf" ;
        ns1:original_cwlVersion  "v1.2" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_snv_bam_readcount_to_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#data_type> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#sample_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#snv_bam_readcount_tsv> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#annotated_bam_readcount_vcf> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_mapq0.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#plugins>
        cwl:inputBinding  [ CommandLineBinding:position
                          9 ] ;
        sld:type          [ cwl:inputBinding  [ CommandLineBinding:prefix
                                              "--plugin" ] ;
                            sld:items         xsd:string ;
                            sld:type          sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_bgzip/file>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/verify_bam_id.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "verify BAM ID" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "--out"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).VerifyBamId" ]
                                 ) ;
        cwl:arguments            ( "--out"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).VerifyBamId" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/local/bin/verifyBamID" ) ;
        cwl:baseCommand          ( "/usr/local/bin/verifyBamID" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/verify_bam_id.cwl#vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/verify_bam_id.cwl#bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/verify_bam_id.cwl#verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/verify_bam_id.cwl#verify_bam_id_depth> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/verify_bam_id-cwl:1.1.3"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/verify_bam_id-cwl:1.1.3"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#artifact_detection_mode>
        sld:type  xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#omni_vcf>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/normalize_variants.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "Normalize variants" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/normalized.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/normalized.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/normalized.vcf.gz" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/normalized.vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/normalize_variants.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/normalize_variants.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/normalize_variants.cwl#normalized_vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  9000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  9000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  9000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  9000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/varscan_somatic.cwl#snvs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "output.snp.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_vep_fields_to_table/tsv>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table/variants_tsv> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#hard_filter/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#processed_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_process_vcf.cwl#index/indexed_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/combine_variants.cwl#combined_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "combined.vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#split_interval_list/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#interval_list> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_depth/minimum_depth>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_minimum_depth> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#all_candidates>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "results/variants/candidateSV.vcf.gz" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_insert_size_metrics.cwl#insert_size_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/align.cwl#readgroup>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file/file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_minimum_depth>
        cwl:default  1 ;
        sld:type     xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/readgroups>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#readgroups> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#pindel/chromosome>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel_cat.cwl#chromosome> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/bams>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bams> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "strelka 2.9.9" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     cwl:valueFrom                "$(inputs.cpu_reserved)"
                                   ]
                                   [ CommandLineBinding:position  2 ;
                                     cwl:valueFrom                "$(runtime.outdir)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/perl" "/usr/bin/docker_helper.pl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#cpu_reserved> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#exome_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#snvs> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/strelka-cwl:2.9.9"
                                 ] ;
        cwl:requirements         [ a                             cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin  4 ;
                                   ResourceRequirement:ramMin    4000
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#reindex/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#remove_end_tags/processed_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_flagstats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/flagstats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mutect_scatter_count>
        sld:type  xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#docm_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#pindel_cat/insert_size>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#insert_size> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr/intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#bqsr_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_p_value>
        cwl:default  9.9e-01 ;
        sld:type     xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/cosmic_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#cosmic_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cat_all.cwl#chromosome_pindel_outs>
        cwl:inputBinding  [ CommandLineBinding:position
                          -1 ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filtered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter/filtered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/target_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#target_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_to_cram.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "BAM to CRAM conversion" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "/opt/samtools/bin/samtools" "view" "-C" ) ;
        cwl:baseCommand          ( "/opt/samtools/bin/samtools" "view" "-C" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_to_cram.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_to_cram.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_to_cram.cwl#cram> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:stdout               "$(inputs.bam.nameroot).cram" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#verify_bam_id_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/verify_bam_id_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#vcf>
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_alignment_summary_metrics.cwl#alignment_summary_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_insert_size_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/insert_size_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vcf_readcount_annotator.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/name_sort.cwl#name_sorted_bam>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).NameSorted.bam" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).NameSorted.bam" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/ensembl_version> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/custom_clinvar_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/ensembl_assembly> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/coding_only> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/ensembl_species> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/synonyms_file> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/cache_dir> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/custom_gnomad_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/plugins> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/vep_summary> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/annotated_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "gathered exome alignment and somatic variant detection" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#gatherer> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_ensembl_species> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#per_base_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#known_indels> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mutect_max_alt_alleles_in_normal_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#normal_readgroups> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#variants_to_table_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#tumor_readgroups> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#picard_metric_accumulation_level> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_strand_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#qc_minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#normal_bams> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#normal_cram_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#strelka_cpu_reserved> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#filter_docm_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mills> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#summary_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#omni_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#variants_to_table_genotype_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#output_dir> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#hgvs_annotation> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#cle_vcf_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#qc_minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#tumor_bams> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#custom_gnomad_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#tumor_cram_name> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#bait_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_cache_dir> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#cosmic_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mutect_artifact_detection_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_min_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_to_table_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#synonyms_file> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_ensembl_assembly> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mutect_scatter_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#bqsr_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#per_target_intervals> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_p_value> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somalier_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mutect_max_alt_allele_in_normal_fraction> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#docm_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#varscan_max_normal_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#pindel_insert_size> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_ensembl_version> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#annotate_coding_only> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#panel_of_normals_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#interval_list> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#final_outputs> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a                           cwl:SchemaDefRequirement ;
                                   SchemaDefRequirement:types  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file>
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#cosmic_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_ensembl_species>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#vep_ensembl_species> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_bgzip>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_bgzip/file> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_bgzip/bgzipped_file> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bgzip.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#mutect_artifact_detection_mode>
        cwl:default  false ;
        sld:type     xsd:boolean .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#hard_filter/output_vcf_basename>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#variant_caller> ;
        cwl:valueFrom  "$(self)_filtered" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/strelka.cwl#snvs>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "results/variants/somatic.snvs.vcf.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#decompose>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#decompose/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#decompose/decomposed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vt_decompose.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/readgroups>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_readgroups> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic_indels>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/somatic> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/metric_accumulation_level>
        cwl:valueFrom  "ALL_READS" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#filter/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "run bam-readcount" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  -3 ;
                                     cwl:valueFrom                "$(runtime.outdir)"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  -3 ;
                                     cwl:valueFrom                "$(runtime.outdir)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/python" "/usr/bin/bam_readcount_helper.py" ) ;
        cwl:baseCommand          ( "/usr/bin/python" "/usr/bin/bam_readcount_helper.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#sample> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#min_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#reference_fasta> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#min_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl#snv_bam_readcount_tsv> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/bam_readcount_helper-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/bam_readcount_helper-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:stdout               "$(inputs.sample)_bam_readcount.tsv" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/align_and_tag.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "align with bwa_mem and tag" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  4 ;
                                     cwl:valueFrom                "$(runtime.cores)"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  4 ;
                                     cwl:valueFrom                "$(runtime.cores)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "/bin/bash" "/usr/bin/alignment_helper.sh" ) ;
        cwl:baseCommand          ( "/bin/bash" "/usr/bin/alignment_helper.sh" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/align_and_tag.cwl#bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/align_and_tag.cwl#readgroup> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/align_and_tag.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/align_and_tag.cwl#aligned_bam> ;
        cwl:requirements         [ a                             cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin  8 ;
                                   ResourceRequirement:ramMin    20000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/alignment_helper-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/alignment_helper-cwl:1.0.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin  8 ;
                                   ResourceRequirement:ramMin    20000
                                 ] ;
        cwl:stdout               "refAlign.bam" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/dbsnp_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#dbsnp_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#tumor_bams>
        sld:type  [ sld:items  cwl:File ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mark_duplicates_and_sort.cwl#sorted_bam>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_name)" ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel_somatic_filter.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#insert_size_histogram>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/insert_size_histogram> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#bam>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "--bam-file"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "--bam-file"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "--bam-file"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "--bam-file"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#process_somatic_indels/variants>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#somatic/indels> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#flagstats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/flagstats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#final_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#index/indexed_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#interval_list>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#all_candidates>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/all_candidates> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_depth>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_depth/minimum_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_depth/sample_names> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_depth/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_vcf_depth/depth_filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_depth.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#somalier_vcf>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/summary_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#summary_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_snv_bam_readcount_tsv>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/snv_bam_readcount_tsv> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_ensembl_assembly>
        rdfs:comment  "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_gnomADe_allele_freq.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "gnomADe_AF filter" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ cwl:valueFrom  "$(inputs.vcf.path)" ]
                                   [ cwl:valueFrom  "$(runtime.outdir)/annotated.af_filtered.vcf" ]
                                   "/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/annotated.af_filtered.vcf" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/perl" "/usr/bin/vcf_check.pl" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_gnomADe_allele_freq.cwl#maximum_population_allele_frequency> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_gnomADe_allele_freq.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/filter_vcf_gnomADe_allele_freq.cwl#filtered_vcf> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/vep_helper-cwl:1.0.0"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#custom_gnomad_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/annotated_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mark_duplicates_and_sort>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mark_duplicates_and_sort/bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mark_duplicates_and_sort/metrics_file> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mark_duplicates_and_sort/sorted_bam> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/mark_duplicates_and_sort.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#target_intervals>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan.cwl#min_coverage>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel_unfiltered_vcf>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel/unfiltered_vcf> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#ensembl_version>
        rdfs:comment      "ensembl version - Must be present in the cache directory. Example: '95'" ;
        cwl:inputBinding  [ CommandLineBinding:position  12 ;
                            CommandLineBinding:prefix    "--cache_version"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/qc_minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#qc_minimum_base_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#per_base_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#gatherer/all_files>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/strelka_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/final_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/final_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/docm_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_mark_duplicates_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_summary_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_mark_duplicates_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_alignment_summary_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_verify_bam_id_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/pindel_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/varscan_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mutect_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/pindel_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_cram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_per_target_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mutect_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_flagstats> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_insert_size_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_cram> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/vep_summary> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_summary_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_alignment_summary_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/final_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_verify_bam_id_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_flagstats> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/tumor_per_base_hs_metrics> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/strelka_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/normal_per_base_coverage_metrics> ;
        cwl:valueFrom  "${ function flatten(inArr, outArr) { var arrLen = inArr.length; for (var i = 0; i < arrLen; i++) { if (Array.isArray(inArr[i])) { flatten(inArr[i], outArr); } else { outArr.push(inArr[i]); } } return outArr; } var no_secondaries = flatten(self, []); var all_files = []; var arrLen = no_secondaries.length; for (var i = 0; i < arrLen; i++) { all_files.push(no_secondaries[i]); var secondaryLen = no_secondaries[i].secondaryFiles.length; for (var j = 0; j < secondaryLen; j++) { all_files.push(no_secondaries[i].secondaryFiles[j]); } } return all_files; }" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/strelka_cpu_reserved>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#strelka_cpu_reserved> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/verify_bam_id.cwl#bam>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--bam" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--bam" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#qc/per_target_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#per_target_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#merge>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#merge/vcfs> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/mutect.cwl#merge/merged_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cat_out.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/bin/cat" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cat_out.cwl#pindel_outs> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cat_out.cwl#pindel_out> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "ubuntu:xenial"
                                 ] ;
        cwl:stdout               "per_chromosome_pindel.out" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel.cwl#tumor_bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/variants_to_table_fields>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#variants_to_table_fields> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/per_base_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#per_base_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine/mutect_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/filtered_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/bait_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#bait_intervals> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/min_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/min_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/reference_fasta> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/sample> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/snv_bam_readcount_tsv> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_readcount.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_vep_fields_to_table.cwl#tsv>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-t" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/strelka_cpu_reserved>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#strelka_cpu_reserved> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/somalier_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somalier_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#somatic_exome/mills>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#mills> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/fp_filter.cwl#filtered_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#apply_bqsr>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#apply_bqsr/bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#apply_bqsr/bqsr_table> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#apply_bqsr/reference> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#apply_bqsr/output_name> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#apply_bqsr/bqsr_bam> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/apply_bqsr.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_docm_variants>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_docm_variants/docm_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_docm_variants/callers_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_docm_variants/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_docm_variants/merged_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_add_variants.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#output_contigs>
        rdfs:comment      "if true, outputs assembled contig sequences in final VCF files, in the INFO field CONTIG" ;
        cwl:inputBinding  [ CommandLineBinding:position  -7 ;
                            CommandLineBinding:prefix    "--outputContig"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file>
        rdfs:label  "a file with a label" ;
        sld:fields  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file/file> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/types/labelled_file.yml#labelled_file/label> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_strelka_gt.cwl#processed_vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "add_gt.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#filter/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/strelka_and_post_processing.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel_insert_size>
        cwl:default  400 ;
        sld:type     xsd:int .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#index>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#index/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#index/indexed_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/index_vcf.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/bam_to_cram.cwl#bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#somaticfilter>
        cwl:in   <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#somaticfilter/pindel_output_summary> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#somaticfilter/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#somaticfilter/vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel_somatic_filter.cwl> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount/sample>
        cwl:default  "TUMOR" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/cat_out.cwl#pindel_out>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "per_chromosome_pindel.out" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/gathered_somatic_exome.cwl#variants_to_table_fields>
        cwl:default  "AC" , "ID" , "ALT" , "CHROM" , "POS" , "REF" , "set" , "AF" ;
        sld:type     [ sld:items  xsd:string ;
                       sld:type   sld:array
                     ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/pindel_somatic_filter.cwl#vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "pindel.out.vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#decompose_variants/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#normalize_variants/normalized_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_strelka_gt.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "add GT tags" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "/usr/bin/perl" "/usr/bin/add_strelka_gt.pl" "$(inputs.vcf.path)" "$(runtime.outdir)" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_strelka_gt.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/add_strelka_gt.cwl#processed_vcf> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/cle:v1.3.1"
                                 ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#filter/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/pindel.cwl#tumor_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#alignment/known_indels>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/exome_alignment.cwl#known_indels> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_bin_level_ratios>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#cnvkit/tumor_bin_level_ratios> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect/scatter_count>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_scatter_count> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/varscan_pre_and_post_processing.cwl#p_value>
        cwl:default  9.9e-01 ;
        sld:type     xsd:float , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#filter_somatic_llr_threshold>
        sld:type  xsd:float .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/filter_vcf.cwl#sample_names>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table/fields>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table_fields> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/collect_hs_metrics.cwl#per_target_coverage_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Detect Variants workflow" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam_readcount> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#combine> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_vep_fields_to_table> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_bgzip> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_docm_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#index> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_tumor_bam_readcount_to_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam_readcount> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#decompose_index> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#decompose> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotated_filter_index> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_normal_bam_readcount_to_vcf> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#custom_clinvar_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#dbsnp_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_strand_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#cosmic_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table_genotype_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_bam> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#cle_vcf_filter> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_ensembl_assembly> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_scatter_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_pick> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#custom_gnomad_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_docm_variants> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#readcount_minimum_mapping_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_min_var_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_max_normal_freq> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#panel_of_normals_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_gnomADe_maximum_population_allele_frequency> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_to_table_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_minimum_depth> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#interval_list> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka_exome_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_mapq0_threshold> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_p_value> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#readcount_minimum_base_quality> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_min_coverage> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_max_alt_alleles_in_normal_count> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#annotate_coding_only> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_ensembl_version> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel_insert_size> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_max_alt_allele_in_normal_fraction> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_plugins> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#variants_to_table_fields> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka_cpu_reserved> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#filter_somatic_llr_threshold> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_ensembl_species> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#synonyms_file> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_artifact_detection_mode> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_cache_dir> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#final_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_indel_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm_filtered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#varscan_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#normal_snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#tumor_snv_bam_readcount_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#vep_summary> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#pindel_unfiltered_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#final_tsv> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#final_vcf> , <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#mutect_filtered_vcf> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_only_variants>
        cwl:outputSource    <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta/tumor_only_variants> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#add_docm_variants/docm_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#docm/docm_variants_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/manta_somatic.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  -4 ;
                            CommandLineBinding:prefix    "--referenceFasta"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_summary_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#tumor_alignment_and_qc/alignment_summary_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/vcf_readcount_annotator.cwl#add_indel_bam_readcount_to_vcf/variant_type>
        cwl:default  "indel" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/hs_metrics.cwl#minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#GATK_haplotype_caller/docm_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/docm_cle.cwl#docm_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/vep.cwl#everything>
        cwl:default       true ;
        cwl:inputBinding  [ CommandLineBinding:position  10 ;
                            CommandLineBinding:prefix    "--everything"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/normalize_variants.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka/cpu_reserved>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/detect_variants.cwl#strelka_cpu_reserved> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#detect_variants/docm_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#docm_vcf> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/final_name>
        cwl:source     <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_name> ;
        cwl:valueFrom  "$(self).bam" .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#manta_call_regions>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File , sld:null .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/qc_exome.cwl#bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#apply_bqsr/bam>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/bam_to_bqsr.cwl#mark_duplicates_and_sort/sorted_bam> .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_summary_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/pipelines/somatic_exome.cwl#normal_alignment_and_qc/summary_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/docm_add_variants.cwl#callers_vcf>
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant:callers"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/tools/merge_bams_samtools.cwl#merged_bam>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.name).merged.bam" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.name).merged.bam" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#fp_filter/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/195b4ab487c939eb32a55d9f78bc1befd100caae/definitions/subworkflows/fp_filter.cwl#index/indexed_vcf> .