@prefix LoadListingRequirement: <http://commonwl.org/cwltool#LoadListingRequirement/> .
@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 ns2:   <http://commonwl.org/cwltool#> .
@prefix ns1:   <https://www.sevenbridges.com/> .
@prefix NetworkAccess: <http://commonwl.org/cwltool#NetworkAccess/> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .
@prefix ResourceRequirement: <https://w3id.org/cwl/cwl#ResourceRequirement/> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups/Sample>
        cwl:inputBinding  [ CommandLineBinding:position  10 ;
                            CommandLineBinding:prefix    "-SM"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_analyzecovariates.cwl#gatk_analyzecovariates/plots_pdf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$*.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastqc>
        rdfs:label  "fastQc" ;
        cwl:in      <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastqc/fastq1> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastqc/fastq2> ;
        cwl:run     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/fastqc.cwl> ;
        ns1:x       1.481406e+02 ;
        ns1:y       2.918516e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_view.cwl#samtools_view>
        a                        cwl:CommandLineTool ;
        rdfs:label               "samtools_view" ;
        ns2:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "" ;
                                     cwl:valueFrom                "-Sb"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "samtools" "view" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_view.cwl#samtools_view/aligned_sam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_view.cwl#samtools_view/aligned_bam> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "biocontainers/samtools:1.3.1"
                                 ] ;
        cwl:stdout               "$(inputs.aligned_sam.nameroot).bam" .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_markduplicates.cwl#picard_markduplicates>
        a                        cwl:CommandLineTool ;
        rdfs:label               "picard_MarkDuplicates" ;
        ns2:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "--REMOVE_DUPLICATES" ;
                                     cwl:valueFrom                "true"
                                   ]
                                   [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "--ASSUME_SORTED" ;
                                     cwl:valueFrom                "true"
                                   ]
                                   [ CommandLineBinding:position  3 ;
                                     CommandLineBinding:prefix    "-O" ;
                                     cwl:valueFrom                "$(inputs.sorted_bam.nameroot).dedup.bam"
                                   ]
                                   [ CommandLineBinding:position  4 ;
                                     CommandLineBinding:prefix    "-M" ;
                                     cwl:valueFrom                "$(inputs.sorted_bam.nameroot).dedup.bam.metrics"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "gatk" "MarkDuplicates" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_markduplicates.cwl#picard_markduplicates/sorted_bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_markduplicates.cwl#picard_markduplicates/metrics> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_markduplicates.cwl#picard_markduplicates/dedup_bam> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "broadinstitute/gatk:4.1.2.0"
                                 ] .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/sample_name>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Sample> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups/Platform>
        cwl:inputBinding  [ CommandLineBinding:position  6 ;
                            CommandLineBinding:prefix    "-PL"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow>
        a                        cwl:Workflow ;
        rdfs:label               "VariantCalling_MutectWithPON_workflow" ;
        ns2:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_markduplicates> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_view> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bwa_mem_0_7_15> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastqc> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_index_bam> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_analyzecovariates> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_sort> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create_1> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bed_file> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gnomad_vcf> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Platform> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastq2> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/sam_name> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Library> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/dbSNP_vcf> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Barcode> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastq1> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/PoN_vcf> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Sample> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/ref_seq> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/metrics> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/vcf> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/plots_pdf> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_view/aligned_sam>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bwa_mem_0_7_15/output_sam> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_analyzecovariates/recal_table>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create/output> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Library>
        sld:type  xsd:string ;
        ns1:x     8.090868e+02 ;
        ns1:y     3.731484e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bed_file>
        sld:type  cwl:File ;
        ns1:x     1.037066e+03 ;
        ns1:y     5.330391e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups>
        a                        cwl:CommandLineTool ;
        rdfs:label               "picard_AddOrReplaceReadGroups" ;
        ns2:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  2 ;
                                     CommandLineBinding:prefix    "-O" ;
                                     cwl:valueFrom                "$(inputs.sorted_dedup_bam.nameroot).RG.bam"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "gatk" "AddOrReplaceReadGroups" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups/Library> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups/Sample> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups/Platform> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups/Barcode> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups/sorted_dedup_bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups/dedup_RG_bam> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "broadinstitute/gatk:4.1.2.0"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl#gatk_bqsr_table_create/dbSNP_vcf>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--known-sites"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--known-sites"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_view.cwl#samtools_view/aligned_sam>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/bed_file>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bed_file> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastqc/fastq1>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastq1> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_analyzecovariates/post_recal_table>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create_1/output> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_sort>
        rdfs:label  "samtools_sort" ;
        cwl:in      <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_sort/aligned_bam> ;
        cwl:out     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_sort/sorted> ;
        cwl:run     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_sort.cwl> ;
        ns1:x       6.155712e+02 ;
        ns1:y       3.731484e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/bwa_mem.cwl#bwa_mem_0_7_15/fastq2>
        rdfs:comment      "optional second fastq file" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/bwa_mem.cwl#bwa_mem_0_7_15/ref_seq>
        rdfs:comment        "reference seq" ;
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/fastqc.cwl#fastqc>
        a                        cwl:CommandLineTool ;
        rdfs:label               "fastQc" ;
        ns2:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "fastqc" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/fastqc.cwl#fastqc/fastq2> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/fastqc.cwl#fastqc/fastq1> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "maxulysse/fastqc:latest"
                                 ] .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_sort/aligned_bam>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_view/aligned_bam> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/Sample>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Sample> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/Platform>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Platform> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/gnomad_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gnomad_vcf> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/vcf>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/vcf> ;
        sld:type          cwl:File ;
        ns1:x             2.158067e+03 ;
        ns1:y             3.731484e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/sam_name>
        sld:type  xsd:string ;
        ns1:x     0 ;
        ns1:y     1.065938e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_analyzecovariates.cwl#gatk_analyzecovariates/recal_table>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-before"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl#gatk_bqsr_table_create/bed_file>
        cwl:inputBinding  [ CommandLineBinding:position  11 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  11 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_sort.cwl#samtools_sort>
        a                        cwl:CommandLineTool ;
        rdfs:label               "samtools_sort" ;
        ns2:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  1 ;
                                     CommandLineBinding:prefix    "-o" ;
                                     cwl:valueFrom                "$(inputs.aligned_bam.nameroot)_sorted.bam"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "samtools" "sort" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_sort.cwl#samtools_sort/aligned_bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_sort.cwl#samtools_sort/sorted> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "biocontainers/samtools:1.3.1"
                                 ] .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl#gatk_bqsr_table_create/bam_dedup_RG>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-I"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-I"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/Library>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Library> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n>
        a                        cwl:CommandLineTool ;
        rdfs:label               "gatk_Mutect2_tumorOnly_with_PoN" ;
        ns2:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "--af-of-alleles-not-in-resource" ;
                                     cwl:valueFrom                "0.00003125"
                                   ]
                                   [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "--f1r2-tar-gz" ;
                                     cwl:valueFrom                "$(inputs.sample_name).f1r2.tar.gz"
                                   ]
                                   [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "-max-reads-per-alignment-start" ;
                                     cwl:valueFrom                "0"
                                   ]
                                   [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "-O" ;
                                     cwl:valueFrom                "$(inputs.sample_name).vcf"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "gatk" "Mutect2" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/sample_name> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/BQSR2_bam> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/PoN_vcf> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/gnomad_vcf> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/ref_fasta> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/bed_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/f1r2> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/vcf> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "broadinstitute/gatk:4.1.2.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin  1 ;
                                   ResourceRequirement:ramMin    8000
                                 ] .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl#gatk_bqsr_table_create>
        a                        cwl:CommandLineTool ;
        rdfs:label               "gatk_BQSR_table_create" ;
        ns2:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  7 ;
                                     CommandLineBinding:prefix    "-O" ;
                                     cwl:valueFrom                "$(inputs.bam_dedup_RG.nameroot).rgb"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  7 ;
                                     CommandLineBinding:prefix    "-O" ;
                                     cwl:valueFrom                "$(inputs.bam_dedup_RG.nameroot).rgb"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "gatk" "BaseRecalibrator" ) ;
        cwl:baseCommand          ( "gatk" "BaseRecalibrator" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl#gatk_bqsr_table_create/ref_file> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl#gatk_bqsr_table_create/bam_dedup_RG> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl#gatk_bqsr_table_create/dbSNP_vcf> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl#gatk_bqsr_table_create/bed_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl#gatk_bqsr_table_create/output> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "broadinstitute/gatk:4.1.2.0"
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "broadinstitute/gatk:4.1.2.0"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bwa_mem_0_7_15/ref_seq>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/ref_seq> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_ApplyBQSR.cwl#gatk__apply_b_q_s_r/bed_file>
        cwl:inputBinding  [ CommandLineBinding:position  11 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_index_bam/bam_file>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/dedup_RG_bam> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/fastqc.cwl#fastqc/fastq1>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bwa_mem_0_7_15/fastq1>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastq1> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastq2>
        sld:type  cwl:File ;
        ns1:x     0 ;
        ns1:y     6.397031e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_sort.cwl#samtools_sort/aligned_bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create_1/ref_file>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/ref_seq> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/bwa_mem.cwl#bwa_mem_0_7_15/sam_name>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/PoN_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/PoN_vcf> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1>
        rdfs:label  "picard_AddOrReplaceReadGroups" ;
        cwl:in      <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/Sample> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/Barcode> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/sorted_dedup_bam> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/Library> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/Platform> ;
        cwl:out     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/dedup_RG_bam> ;
        cwl:run     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl> ;
        ns1:x       1.037066e+03 ;
        ns1:y       1.852578e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/sample_name>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "-tumor"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create_1/bam_dedup_RG>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r/output_bqsr_bam> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/gnomad_vcf>
        cwl:inputBinding  [ CommandLineBinding:position  7 ;
                            CommandLineBinding:prefix    "--germline-resource"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create_1/dbSNP_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/dbSNP_vcf> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/ref_fasta>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_analyzecovariates.cwl#gatk_analyzecovariates/post_recal_table>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "-after"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups/Barcode>
        cwl:inputBinding  [ CommandLineBinding:position  8 ;
                            CommandLineBinding:prefix    "-PU"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create_1/bed_file>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bed_file> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gnomad_vcf>
        sld:type  cwl:File ;
        ns1:x     0 ;
        ns1:y     5.330391e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups/sorted_dedup_bam>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-I"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create/dbSNP_vcf>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/dbSNP_vcf> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_markduplicates/metrics> ;
        sld:type          cwl:File ;
        ns1:x             1.037066e+03 ;
        ns1:y             3.198516e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastqc/fastq2>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastq2> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r/ref_file>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/ref_seq> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_markduplicates.cwl#picard_markduplicates/sorted_bam>
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "-I"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create/bam_dedup_RG>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/dedup_RG_bam> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create/bed_file>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bed_file> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/vcf_name>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Sample> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl#gatk_bqsr_table_create/ref_file>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/Barcode>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Barcode> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/bwa_mem.cwl#bwa_mem_0_7_15/output_sam>
        rdfs:comment       "Alignments in SAM format" ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sam_name)" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r>
        rdfs:label  "gatk_ApplyBQSR" ;
        cwl:in      <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r/bam_dedup_RG> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r/bed_file> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r/recal_data_table> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r/ref_file> ;
        cwl:out     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r/output_bqsr_bam> ;
        cwl:run     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_ApplyBQSR.cwl> ;
        ns1:x       1.59279e+03 ;
        ns1:y       4.264453e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/PoN_vcf>
        sld:type  cwl:File ;
        ns1:x     0 ;
        ns1:y     3.197812e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/ref_seq>
        sld:type  cwl:File ;
        ns1:x     0 ;
        ns1:y     2.131875e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r/bed_file>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bed_file> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Sample>
        sld:type  xsd:string ;
        ns1:x     0 ;
        ns1:y     0 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_view>
        rdfs:label  "samtools_view" ;
        cwl:in      <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_view/aligned_sam> ;
        cwl:out     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_view/aligned_bam> ;
        cwl:run     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_view.cwl> ;
        ns1:x       3.88243e+02 ;
        ns1:y       3.731484e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r/recal_data_table>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create/output> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_ApplyBQSR.cwl#gatk__apply_b_q_s_r/ref_file>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups/Library>
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "-LB"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Platform>
        sld:type  xsd:string ;
        ns1:x     0 ;
        ns1:y     4.26375e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/BQSR2_bam>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r/output_bqsr_bam> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/vcf>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sample_name).vcf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/sorted_dedup_bam>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_markduplicates/dedup_bam> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/fastqc.cwl#fastqc/fastq2>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_index_bam.cwl#samtools_index_bam/bam_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          0 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bwa_mem_0_7_15/fastq2>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastq2> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/PoN_vcf>
        cwl:inputBinding  [ CommandLineBinding:position  9 ;
                            CommandLineBinding:prefix    "--panel-of-normals"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bwa_mem_0_7_15/sam_name>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/sam_name> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_markduplicates.cwl#picard_markduplicates/dedup_bam>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sorted_bam.nameroot).dedup.bam" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_index_bam.cwl#samtools_index_bam>
        a                        cwl:CommandLineTool ;
        rdfs:label               "samtools_index_bam" ;
        ns2:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "samtools" "index" "-b" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_index_bam.cwl#samtools_index_bam/bam_file> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "biocontainers/samtools:1.3.1"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:stdout               "$(inputs.bam_file.basename).bai" .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create>
        rdfs:label  "gatk_BQSR_table_create" ;
        cwl:in      <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create/ref_file> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create/bed_file> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create/bam_dedup_RG> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create/dbSNP_vcf> ;
        cwl:out     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create/output> ;
        cwl:run     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl> ;
        ns1:x       1.353328e+03 ;
        ns1:y       4.264453e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/plots_pdf>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_analyzecovariates/plots_pdf> ;
        sld:type          cwl:File ;
        ns1:x             1.904645e+03 ;
        ns1:y             2.034141e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/dbSNP_vcf>
        sld:type  cwl:File ;
        ns1:x     1.037066e+03 ;
        ns1:y     4.264453e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/f1r2>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sample_name).f1r2.tar.gz" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_sort.cwl#samtools_sort/sorted>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*_sorted.bam" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_view.cwl#samtools_view/aligned_bam>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.bam" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_markduplicates.cwl#picard_markduplicates/metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.sorted_bam.nameroot).dedup.bam.metrics" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_markduplicates/sorted_bam>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_sort/sorted> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/ref_fasta>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/ref_seq> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/bwa_mem.cwl#bwa_mem_0_7_15/fastq1>
        rdfs:comment      "fastq" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create_1>
        rdfs:label  "gatk_BQSR_table_create" ;
        cwl:in      <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create_1/bed_file> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create_1/dbSNP_vcf> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create_1/bam_dedup_RG> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create_1/ref_file> ;
        cwl:out     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create_1/output> ;
        cwl:run     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl> ;
        ns1:x       1.904645e+03 ;
        ns1:y       5.218125e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_ApplyBQSR.cwl#gatk__apply_b_q_s_r>
        a                        cwl:CommandLineTool ;
        rdfs:label               "gatk_ApplyBQSR" ;
        ns2:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  7 ;
                                     CommandLineBinding:prefix    "-O" ;
                                     cwl:valueFrom                "$(inputs.bam_dedup_RG.nameroot).BQSR.bam"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "gatk" "ApplyBQSR" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_ApplyBQSR.cwl#gatk__apply_b_q_s_r/ref_file> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_ApplyBQSR.cwl#gatk__apply_b_q_s_r/bam_dedup_RG> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_ApplyBQSR.cwl#gatk__apply_b_q_s_r/bed_file> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_ApplyBQSR.cwl#gatk__apply_b_q_s_r/recal_data_table> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_ApplyBQSR.cwl#gatk__apply_b_q_s_r/output_bqsr_bam> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "broadinstitute/gatk:4.1.2.0"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_index_bam>
        rdfs:label  "samtools_index_bam" ;
        cwl:in      <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/samtools_index_bam/bam_file> ;
        cwl:run     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/samtools_index_bam.cwl> ;
        ns1:x       1.353328e+03 ;
        ns1:y       2.987812e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_ApplyBQSR.cwl#gatk__apply_b_q_s_r/recal_data_table>
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "-bqsr"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_ApplyBQSR.cwl#gatk__apply_b_q_s_r/output_bqsr_bam>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam_dedup_RG.nameroot).BQSR.bam" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/BQSR2_bam>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-I"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/Barcode>
        sld:type  xsd:string ;
        ns1:x     8.090868e+02 ;
        ns1:y     4.798125e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_ApplyBQSR.cwl#gatk__apply_b_q_s_r/bam_dedup_RG>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-I"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_analyzecovariates>
        rdfs:label  "gatk_AnalyzeCovariates" ;
        cwl:in      <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_analyzecovariates/post_recal_table> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_analyzecovariates/recal_table> ;
        cwl:out     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_analyzecovariates/plots_pdf> ;
        cwl:run     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_analyzecovariates.cwl> ;
        ns1:x       1.59279e+03 ;
        ns1:y       2.917109e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_bqsr_table_create.cwl#gatk_bqsr_table_create/output>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam_dedup_RG.nameroot).rgb" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam_dedup_RG.nameroot).rgb" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_bqsr_table_create/ref_file>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/ref_seq> .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_addorreplacereadgroups.cwl#picard_addorreplacereadgroups/dedup_RG_bam>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*RG.bam" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bwa_mem_0_7_15>
        rdfs:label  "bwa mem v0.7.5" ;
        cwl:in      <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bwa_mem_0_7_15/sam_name> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bwa_mem_0_7_15/fastq2> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bwa_mem_0_7_15/fastq1> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bwa_mem_0_7_15/ref_seq> ;
        cwl:out     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/bwa_mem_0_7_15/output_sam> ;
        cwl:run     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/bwa_mem.cwl> ;
        ns1:x       1.481406e+02 ;
        ns1:y       4.264453e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n>
        rdfs:label  "gatk_Mutect2_tumorOnly_with_PoN" ;
        cwl:in      <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/PoN_vcf> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/bed_file> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/ref_fasta> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/vcf_name> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/sample_name> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/gnomad_vcf> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/BQSR2_bam> ;
        cwl:out     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk_mutect2_tumoronly_with__po_n/vcf> ;
        cwl:run     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl> ;
        ns1:x       1.904645e+03 ;
        ns1:y       3.520781e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/bwa_mem.cwl#bwa_mem_0_7_15>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "BwaMem" ;
        rdfs:label               "bwa mem v0.7.5" ;
        ns2:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "" ;
                                     cwl:valueFrom                "-M"
                                   ]
                                   [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "" ;
                                     cwl:valueFrom                "-a"
                                   ]
                                   [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "-v" ;
                                     cwl:valueFrom                "3"
                                   ]
                                   [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "-t" ;
                                     cwl:valueFrom                "20"
                                   ]
                                   [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "-k" ;
                                     cwl:valueFrom                "20"
                                   ]
                                   [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "-r" ;
                                     cwl:valueFrom                "0.02"
                                   ]
                                   [ CommandLineBinding:position  0 ;
                                     CommandLineBinding:prefix    "-w" ;
                                     cwl:valueFrom                "200"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "bwa" "mem" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/bwa_mem.cwl#bwa_mem_0_7_15/sam_name> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/bwa_mem.cwl#bwa_mem_0_7_15/ref_seq> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/bwa_mem.cwl#bwa_mem_0_7_15/fastq2> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/bwa_mem.cwl#bwa_mem_0_7_15/fastq1> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/bwa_mem.cwl#bwa_mem_0_7_15/output_sam> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                             cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin  8 ;
                                   ResourceRequirement:ramMin    10000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "biocontainers/bwa:0.7.15"
                                 ] ;
        cwl:stdout               "$(inputs.sam_name)" .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_analyzecovariates.cwl#gatk_analyzecovariates>
        a                        cwl:CommandLineTool ;
        rdfs:label               "gatk_AnalyzeCovariates" ;
        ns2:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( [ CommandLineBinding:position  6 ;
                                     CommandLineBinding:prefix    "-plots" ;
                                     cwl:valueFrom                "$(inputs.recal_table.nameroot).plots.pdf"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "gatk" "AnalyzeCovariates" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_analyzecovariates.cwl#gatk_analyzecovariates/post_recal_table> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_analyzecovariates.cwl#gatk_analyzecovariates/recal_table> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_analyzecovariates.cwl#gatk_analyzecovariates/plots_pdf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "broadinstitute/gatk:4.1.2.0"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/gatk_mutect2_tumoronly_with_PoN.cwl#gatk_mutect2_tumoronly_with__po_n/bed_file>
        cwl:inputBinding  [ CommandLineBinding:position  11 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_markduplicates>
        rdfs:label  "picard_MarkDuplicates" ;
        cwl:in      <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_markduplicates/sorted_bam> ;
        cwl:out     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_markduplicates/dedup_bam> , <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_markduplicates/metrics> ;
        cwl:run     <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/picard_markduplicates.cwl> ;
        ns1:x       8.090868e+02 ;
        ns1:y       2.594844e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/fastq1>
        sld:type  cwl:File ;
        ns1:x     0 ;
        ns1:y     7.462969e+02 .

<https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/gatk__apply_b_q_s_r/bam_dedup_RG>
        cwl:source  <https://w3id.org/cwl/view/git/ffff3e8d2310ff23766ce91ab04c7515518303b5/VariantCalling_MutectWithPON_workflow.cwl#_variant_calling__mutect_with_p_o_n_workflow/picard_addorreplacereadgroups_1/dedup_RG_bam> .