@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 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 cwl:   <https://w3id.org/cwl/cwl#> .
@prefix ResourceRequirement: <https://w3id.org/cwl/cwl#ResourceRequirement/> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_target_coverage>
        cwl:outputSource  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/normal_target_coverage> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#male_reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-y" ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#intervals_target>
        cwl:outputSource  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/intervals_target> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/bait_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#bait_intervals> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/drop_low_coverage>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#drop_low_coverage> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#method>
        sld:type  xsd:string , sld:null .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#tumor_bam>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/method>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#method> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_cram>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#scatter_plot>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/diagram>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#diagram> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#intervals_antitarget>
        cwl:outputSource  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/intervals_antitarget> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cram_to_bam.cwl#bam>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.cram.nameroot).bam" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.cram.nameroot).bam" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_cram>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#access>
        sld:type  cwl:File , sld:null .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#reference_cnn>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "-r" ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_antitarget_coverage>
        cwl:outputSource  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/tumor_antitarget_coverage> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#diagram>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_segmented_ratios>
        cwl:outputSource  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/tumor_segmented_ratios> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/access>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#access> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cram_to_bam.cwl#cram>
        cwl:inputBinding    [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding    [ CommandLineBinding:position
                          2 ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_cram_to_bam>
        cwl:in   <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_cram_to_bam/cram> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_cram_to_bam/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_cram_to_bam/bam> ;
        cwl:run  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cram_to_bam.cwl> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_cram_to_bam/cram>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_cram> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_cram_to_bam/cram>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_cram> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cram_to_bam.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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#bait_intervals>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/reference>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#reference> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cram_to_bam.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "samtools view cram to bam" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.cram.nameroot).bam" ]
                                 ) ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.cram.nameroot).bam" ]
                                 ) ;
        cwl:baseCommand          ( "/opt/samtools/bin/samtools" "view" "-b" ) ;
        cwl:baseCommand          ( "/opt/samtools/bin/samtools" "view" "-b" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cram_to_bam.cwl#cram> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cram_to_bam.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cram_to_bam.cwl#bam> ;
        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"
                                 ] .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Subworkflow to allow calling cnvkit with cram instead of bam files" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_cram_to_bam> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_cram_to_bam> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#method> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_cram> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_cram> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#access> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#drop_low_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#reference> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#diagram> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#scatter_plot> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#bait_intervals> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_target_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_antitarget_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_target_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_antitarget_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_bin_level_ratios> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#intervals_target> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_segmented_ratios> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#cn_scatter_plot> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#intervals_antitarget> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#cn_diagram> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#reference_coverage> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/scatter_plot>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#scatter_plot> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/normal_bam>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_cram_to_bam/bam> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/tumor_bam>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_cram_to_bam/bam> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#cn_diagram>
        cwl:outputSource  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/cn_diagram> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#drop_low_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#access> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#diagram> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#bait_intervals> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#scatter_plot> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#tumor_bam> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#reference_cnn> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#reference> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#method> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#normal_bam> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#male_reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#normal_target_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#intervals_antitarget> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#intervals_target> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#tumor_target_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#normal_antitarget_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#tumor_segmented_ratios> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#reference_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#cn_diagram> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#cn_scatter_plot> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#tumor_antitarget_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl#tumor_bin_level_ratios> ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "etal/cnvkit:0.9.5"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:ramMin     4000 ;
                                   ResourceRequirement:tmpdirMin  10000
                                 ] .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_target_coverage>
        cwl:outputSource  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/tumor_target_coverage> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_cram_to_bam>
        cwl:in   <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_cram_to_bam/reference> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_cram_to_bam/cram> ;
        cwl:out  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_cram_to_bam/bam> ;
        cwl:run  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cram_to_bam.cwl> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#drop_low_coverage>
        sld:type  xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_cram_to_bam/reference>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#reference> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#cn_scatter_plot>
        cwl:outputSource  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/cn_scatter_plot> ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_cram_to_bam/reference>
        cwl:source  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#reference> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit>
        cwl:in   <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/drop_low_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/diagram> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/bait_intervals> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/reference> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/access> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/normal_bam> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/scatter_plot> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/tumor_bam> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/method> ;
        cwl:out  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/normal_target_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/cn_scatter_plot> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/tumor_segmented_ratios> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/reference_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/intervals_target> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/intervals_antitarget> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/normal_antitarget_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/tumor_target_coverage> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/cn_diagram> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/tumor_bin_level_ratios> , <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/tumor_antitarget_coverage> ;
        cwl:run  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/tools/cnvkit_batch.cwl> .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#tumor_bin_level_ratios>
        cwl:outputSource  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/tumor_bin_level_ratios> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#normal_antitarget_coverage>
        cwl:outputSource  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/normal_antitarget_coverage> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/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/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#reference_coverage>
        cwl:outputSource  <https://w3id.org/cwl/view/git/869b331cfeb9dbd5907498e3eccdebc7c28283e5/definitions/subworkflows/cram_to_cnvkit.cwl#run_cnvkit/reference_coverage> ;
        sld:type          cwl:File , sld:null .