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

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/metric_accumulation_level>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#picard_metric_accumulation_level> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#per_target_coverage>
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_TARGET_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_TARGET_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_TARGET_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_TARGET_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#minimum_base_quality> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "Exome QC workflow" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#select_variants> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#samtools_flagstat> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#target_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#reference> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#summary_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_target_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#bam> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_base_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#minimum_mapping_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#bait_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#minimum_base_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#omni_vcf> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#picard_metric_accumulation_level> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#summary_hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_base_hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#alignment_summary_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_target_hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#flagstats> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id_depth> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#insert_size_histogram> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#insert_size_metrics> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a                           cwl:SchemaDefRequirement ;
                                   SchemaDefRequirement:types  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file>
                                 ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_alignment_summary_metrics.cwl#alignment_summary_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_base_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#bam> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#bait_intervals>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "BAIT_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "BAIT_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "BAIT_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "BAIT_INTERVALS=" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl#filtered_vcf>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.output_vcf_basename).vcf.gz" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#minimum_base_quality>
        cwl:default       1 ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_BASE_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_BASE_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_BASE_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_BASE_QUALITY=" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_insert_size_metrics.cwl#insert_size_histogram>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics>
        cwl:in             <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/minimum_base_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/output_prefix> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/target_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/per_target_coverage> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/bait_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/reference> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/per_base_coverage> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/bam> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/minimum_mapping_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/metric_accumulation_level> ;
        cwl:out            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/hs_metrics> ;
        cwl:run            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/bait_intervals> <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/target_intervals> <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/output_prefix> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_insert_size_metrics.cwl#insert_size_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#target_intervals>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "TARGET_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "TARGET_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "TARGET_INTERVALS=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "TARGET_INTERVALS=" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id>
        cwl:in   <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id/vcf> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id/bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id/verify_bam_id_depth> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id/verify_bam_id_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/verify_bam_id.cwl> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/output_prefix>
        cwl:source     <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_target_intervals> ;
        cwl:valueFrom  "target-$(self.label)" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_target_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_target_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/metric_accumulation_level>
        cwl:valueFrom  "ALL_READS" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#reference> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#minimum_base_quality> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#output_prefix>
        cwl:default  "out" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#per_base_coverage>
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_BASE_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_BASE_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_BASE_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix  "PER_BASE_COVERAGE=" ;
                            cwl:valueFrom              "${\n    if(self) {\n        return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n    } else {\n        return false;\n    }\n}\n"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/verify_bam_id.cwl#verify_bam_id_depth>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).VerifyBamId.depthSM" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#target_intervals>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file/file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#bam> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#samtools_flagstat>
        cwl:in   <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#samtools_flagstat/bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#samtools_flagstat/flagstats> ;
        cwl:run  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/samtools_flagstat.cwl> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "collect HS metrics" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
                                 ) ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
                                 ) ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
                                 ) ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#bam> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#minimum_base_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#bait_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#reference> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#per_base_coverage> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#per_target_coverage> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#target_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#metric_accumulation_level> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#output_prefix> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#minimum_mapping_quality> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#per_base_coverage_metrics> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  52000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  52000
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  52000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  52000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics>
        cwl:in   <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/bait_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/per_base_coverage> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/bam> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/output_prefix> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/minimum_base_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/minimum_mapping_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/target_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/metric_accumulation_level> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/reference> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/per_target_coverage> ;
        cwl:out  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/hs_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#per_base_coverage_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-R"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/target_intervals>
        cwl:source     <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_target_intervals> ;
        cwl:valueFrom  "$(self.file)" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#bam> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/metric_accumulation_level>
        cwl:valueFrom  "ALL_READS" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#bam> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_target_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_target_intervals> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_alignment_summary_metrics.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "REFERENCE_SEQUENCE=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#minimum_base_quality> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_target_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_target_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#summary_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl#output_vcf_basename>
        cwl:default  "select_variants" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#insert_size_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/insert_size_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#omni_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file/label>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#alignment_summary_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/alignment_summary_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#bam> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics>
        cwl:in   <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/bam> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/metric_accumulation_level> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/alignment_summary_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_alignment_summary_metrics.cwl> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/per_target_coverage>
        cwl:default  true .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#hs_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/hs_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#picard_metric_accumulation_level>
        cwl:default  "ALL_READS" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#summary_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/summary_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/verify_bam_id.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--vcf" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_alignment_summary_metrics.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "INPUT=" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#minimum_mapping_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#flagstats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#samtools_flagstat/flagstats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/bait_intervals>
        cwl:source     <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_target_intervals> ;
        cwl:valueFrom  "$(self.file)" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/output_prefix>
        cwl:source     <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_base_intervals> ;
        cwl:valueFrom  "base-$(self.label)" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/target_intervals>
        cwl:source     <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_base_intervals> ;
        cwl:valueFrom  "$(self.file)" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_target_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/target_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#target_intervals> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#bam> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/per_base_coverage>
        cwl:default  false .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_base_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/per_base_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/verify_bam_id.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "verify BAM ID" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "--out"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).VerifyBamId" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/local/bin/verifyBamID" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/verify_bam_id.cwl#vcf> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/verify_bam_id.cwl#bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/verify_bam_id.cwl#verify_bam_id_depth> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/verify_bam_id.cwl#verify_bam_id_metrics> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/verify_bam_id-cwl:1.1.3"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics>
        cwl:in             <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/bait_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/bam> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/target_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/metric_accumulation_level> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/per_target_coverage> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/output_prefix> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/minimum_mapping_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/minimum_base_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/per_base_coverage> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/reference> ;
        cwl:out            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/hs_metrics> ;
        cwl:run            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/bait_intervals> <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/target_intervals> <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/output_prefix> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_insert_size_metrics.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "REFERENCE_SEQUENCE=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#select_variants/filtered_vcf> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/per_base_coverage>
        cwl:default  false .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#minimum_base_quality> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/bam>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#bam> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/output_prefix>
        cwl:source     <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#summary_intervals> ;
        cwl:valueFrom  "summary-$(self.label)" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics>
        cwl:in   <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/bam> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/minimum_base_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/minimum_mapping_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/summary_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_target_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/reference> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_base_intervals> ;
        cwl:out  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_target_hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_base_hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/summary_hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_target_coverage_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#select_variants/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#omni_vcf> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/metric_accumulation_level>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#picard_metric_accumulation_level> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_base_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_base_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_alignment_summary_metrics.cwl#metric_accumulation_level>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/verify_bam_id.cwl#verify_bam_id_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).VerifyBamId.selfSM" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_target_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_base_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_alignment_summary_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/samtools_flagstat.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "samtools flagstat" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:baseCommand          ( "/opt/samtools/bin/samtools" "flagstat" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/samtools_flagstat.cwl#bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/samtools_flagstat.cwl#flagstats> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/samtools-cwl:1.0.0"
                                 ] ;
        cwl:stdout               "$(inputs.bam.basename).flagstat" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#summary_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#samtools_flagstat/bam>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#bam> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#minimum_mapping_quality>
        cwl:default       1 ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_MAPPING_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_MAPPING_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_MAPPING_QUALITY=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "MINIMUM_MAPPING_QUALITY=" ] ;
        sld:type          xsd:int , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/per_base_coverage>
        cwl:default  true .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id_depth>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id/verify_bam_id_depth> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/bait_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#bait_intervals> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#select_variants/reference>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#reference> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_alignment_summary_metrics.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "collect alignment summary metrics" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "OUTPUT="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_alignment_summary_metrics.cwl#metric_accumulation_level> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_alignment_summary_metrics.cwl#reference> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_alignment_summary_metrics.cwl#bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_alignment_summary_metrics.cwl#alignment_summary_metrics> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  18000
                                 ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_base_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_base_hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_insert_size_metrics.cwl#metric_accumulation_level>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/per_base_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#per_base_intervals> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_base_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_insert_size_metrics.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "collect insert size metrics" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeMetrics.txt" ]
                                   "H="
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_insert_size_metrics.cwl#bam> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_insert_size_metrics.cwl#reference> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_insert_size_metrics.cwl#metric_accumulation_level> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_insert_size_metrics.cwl#insert_size_histogram> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_insert_size_metrics.cwl#insert_size_metrics> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/picard-cwl:2.18.1"
                                 ] ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  18000
                                 ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#select_variants>
        cwl:in   <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#select_variants/interval_list> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#select_variants/reference> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#select_variants/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#select_variants/filtered_vcf> ;
        cwl:run  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#select_variants/interval_list>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#target_intervals> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/target_intervals>
        cwl:source     <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#summary_intervals> ;
        cwl:valueFrom  "$(self.file)" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_target_coverage_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/per_target_coverage_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#reference> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#minimum_base_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_insert_size_metrics.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/samtools_flagstat.cwl#bam>
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#bam>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/bait_intervals>
        cwl:source     <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_base_intervals> ;
        cwl:valueFrom  "$(self.file)" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#metric_accumulation_level>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#reference> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/minimum_base_quality>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#minimum_base_quality> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/verify_bam_id.cwl#bam>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--bam" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file>
        rdfs:label  "a file with a label" ;
        sld:fields  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file/label> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file/file> ;
        sld:type    sld:record .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl#per_target_coverage_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ;
        sld:type           cwl:File , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#summary_hs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/hs_metrics> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl#exclude_filtered>
        cwl:inputBinding  [ CommandLineBinding:position  4 ;
                            CommandLineBinding:prefix    "--excludeFiltered"
                          ] ;
        sld:type          xsd:boolean , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "SelectVariants (GATK 3.6)" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl#output_vcf_basename> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl#interval_list> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl#vcf> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl#reference> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl#exclude_filtered> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl#filtered_vcf> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "mgibio/gatk-cwl:3.6.0"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin     6000 ;
                                   ResourceRequirement:tmpdirMin  25000
                                 ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/per_base_coverage>
        cwl:default  false .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/minimum_mapping_quality>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#minimum_mapping_quality> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#insert_size_histogram>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/insert_size_histogram> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/samtools_flagstat.cwl#flagstats>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.bam.basename).flagstat" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/per_target_coverage>
        cwl:default  false .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#minimum_mapping_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_detailed_hs_metrics/summary_intervals>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#summary_intervals> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#minimum_base_quality>
        sld:type  xsd:int , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/metric_accumulation_level>
        cwl:valueFrom  "ALL_READS" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id/bam>
        cwl:source  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#bam> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl#vcf>
        cwl:inputBinding    [ CommandLineBinding:position  2 ;
                              CommandLineBinding:prefix    "--variant"
                            ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "HS Metrics workflow" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_target_hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#reference> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_base_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#minimum_mapping_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_target_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#summary_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#minimum_base_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_target_coverage_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_base_hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#summary_hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_base_coverage_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_target_hs_metrics> ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] ;
        cwl:requirements         [ a                           cwl:SchemaDefRequirement ;
                                   SchemaDefRequirement:types  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file>
                                 ] ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_roi_hs_metrics/output_prefix>
        cwl:valueFrom  "roi" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/select_variants.cwl#interval_list>
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "-L"
                          ] ;
        sld:type          cwl:File , sld:null .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#bait_intervals>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics>
        cwl:in             <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/output_prefix> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/reference> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/bam> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/per_base_coverage> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/metric_accumulation_level> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/bait_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/target_intervals> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/per_target_coverage> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/minimum_mapping_quality> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/minimum_base_quality> ;
        cwl:out            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/hs_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/per_base_coverage_metrics> ;
        cwl:run            <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_hs_metrics.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/bait_intervals> <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/target_intervals> <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/output_prefix> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/bait_intervals>
        cwl:source     <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#summary_intervals> ;
        cwl:valueFrom  "$(self.file)" .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_summary_hs_metrics/per_target_coverage>
        cwl:default  false .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#per_target_intervals>
        sld:type  [ sld:items  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/types/labelled_file.yml#labelled_file> ;
                    sld:type   sld:array
                  ] .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#verify_bam_id/verify_bam_id_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/per_target_coverage>
        cwl:default  false .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics>
        cwl:in   <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/bam> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/reference> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/metric_accumulation_level> ;
        cwl:out  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/insert_size_metrics> , <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/qc_exome.cwl#collect_insert_size_metrics/insert_size_histogram> ;
        cwl:run  <https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/tools/collect_insert_size_metrics.cwl> .

<https://w3id.org/cwl/view/git/70e05adeda8b3b4c77b8947266684ce4305db6ac/definitions/subworkflows/hs_metrics.cwl#collect_per_base_hs_metrics/metric_accumulation_level>
        cwl:valueFrom  "ALL_READS" .