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

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/detect_variants/index_bam.cwl#indexed_bam>
        cwl:outputBinding   [ CommandOutputBinding:glob
                          "$(inputs.bam.basename)" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#cram_to_bam/reference>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#reference> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_wgs_metrics.cwl#cram>
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/cram_to_bam.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-T"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#intervals>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/samtools_flagstat.cwl#cram>
        cwl:inputBinding    [ CommandLineBinding:position
                          1 ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id/vcf>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#omni_vcf> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/verify_bam_id.cwl#vcf>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--vcf" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#index_bam>
        cwl:in   <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#index_bam/bam> ;
        cwl:out  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#index_bam/indexed_bam> ;
        cwl:run  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/detect_variants/index_bam.cwl> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/cram>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/cram_to_bam.cwl#cram>
        cwl:inputBinding    [ CommandLineBinding:position
                          2 ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#cram_to_bam>
        cwl:in   <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#cram_to_bam/cram> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#cram_to_bam/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#cram_to_bam/bam> ;
        cwl:run  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/cram_to_bam.cwl> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/metric_accumulation_level>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#picard_metric_accumulation_level> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/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)/AlignmentSummaryMetrics.txt" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_alignment_summary_metrics.cwl#metric_accumulation_level> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_alignment_summary_metrics.cwl#cram> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_alignment_summary_metrics.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_alignment_summary_metrics.cwl#alignment_summary_metrics> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  16000
                                 ] .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_wgs_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#reference> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "WGS QC workflow" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram_to_bam> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#samtools_flagstat> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_alignment_summary_metrics> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_wgs_metrics> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_insert_size_metrics> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#picard_metric_accumulation_level> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#omni_vcf> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#reference> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#intervals> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#gc_bias_metrics_summary> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id_depth> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#insert_size_metrics> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#flagstats> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#gc_bias_metrics_chart> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#wgs_metrics> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#gc_bias_metrics> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#alignment_summary_metrics> ;
        cwl:requirements         [ a  cwl:SubworkflowFeatureRequirement ] .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#bam>
        cwl:outputSource    <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#index_bam/indexed_bam> ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id/verify_bam_id_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id/bam>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram_to_bam/bam> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_wgs_metrics/cram>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id_depth>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id/verify_bam_id_depth> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_alignment_summary_metrics/metric_accumulation_level>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#picard_metric_accumulation_level> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/cram_to_bam.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "samtools view cram to bam" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "-o"
                                   [ cwl:valueFrom  "$(runtime.outdir)/output.bam" ]
                                 ) ;
        cwl:baseCommand          ( "/opt/samtools/bin/samtools" "view" "-b" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/cram_to_bam.cwl#cram> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/cram_to_bam.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/cram_to_bam.cwl#bam> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_wgs_metrics.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_insert_size_metrics>
        cwl:in   <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_insert_size_metrics/cram> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_insert_size_metrics/metric_accumulation_level> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_insert_size_metrics/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_insert_size_metrics/insert_size_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_insert_size_metrics.cwl> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/detect_variants/index_bam.cwl#bam>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics>
        cwl:in   <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/reference> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/metric_accumulation_level> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/cram> ;
        cwl:out  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/gc_bias_metrics> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/gc_bias_metrics_chart> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/gc_bias_metrics_summary> ;
        cwl:run  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#cram_to_bam/cram>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#cram> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#wgs_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_wgs_metrics/wgs_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#gc_bias_metrics_chart>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/gc_bias_metrics_chart> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/detect_variants/index_bam.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "samtools index" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "cp" "$(inputs.bam.path)" "$(runtime.outdir)/$(inputs.bam.basename)"
                                   [ CommandLineBinding:shellQuote  false ;
                                     cwl:valueFrom                  " && "
                                   ]
                                   "/opt/samtools/bin/samtools" "index" "$(inputs.bam.path)" "$(runtime.outdir)/$(inputs.bam.basename).bai"
                                 ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/detect_variants/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/detect_variants/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/detect_variants/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/detect_variants/index_bam.cwl#bam> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/detect_variants/index_bam.cwl#indexed_bam> ;
        cwl:requirements         [ a  cwl:ShellCommandRequirement ] .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#alignment_summary_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_alignment_summary_metrics/alignment_summary_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram_to_bam>
        cwl:in   <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram_to_bam/cram> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram_to_bam/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram_to_bam/bam> ;
        cwl:run  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/verify_bam_id.cwl#verify_bam_id_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "VerifyBamId.selfSM" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id>
        cwl:in   <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id/bam> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id/vcf> ;
        cwl:out  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id/verify_bam_id_depth> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id/verify_bam_id_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/verify_bam_id.cwl> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_insert_size_metrics.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "REFERENCE_SEQUENCE=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram_to_bam/cram>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#reference> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl#metric_accumulation_level>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram_to_bam/reference>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#reference> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/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/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/samtools_flagstat.cwl#cram> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/samtools_flagstat.cwl#flagstats> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] ;
        cwl:stdout               "flagstat.out" .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/verify_bam_id.cwl#verify_bam_id_depth>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "VerifyBamId.depthSM" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_wgs_metrics.cwl#intervals>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "INTERVALS=" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#flagstats>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#samtools_flagstat/flagstats> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "collect gc bias metrics" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/GcBiasMetrics.txt" ]
                                   "CHART="
                                   [ cwl:valueFrom  "$(runtime.outdir)/GcBiasMetricsChart.pdf" ]
                                   "S="
                                   [ cwl:valueFrom  "$(runtime.outdir)/GcBiasMetricsSummary.txt" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectGcBiasMetrics" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl#cram> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl#metric_accumulation_level> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl#gc_bias_metrics> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl#gc_bias_metrics_summary> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl#gc_bias_metrics_chart> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  16000
                                 ] .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_wgs_metrics.cwl#wgs_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "WgsMetrics.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_alignment_summary_metrics>
        cwl:in   <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_alignment_summary_metrics/cram> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_alignment_summary_metrics/reference> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_alignment_summary_metrics/metric_accumulation_level> ;
        cwl:out  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_alignment_summary_metrics/alignment_summary_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_alignment_summary_metrics.cwl> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_alignment_summary_metrics.cwl#alignment_summary_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "AlignmentSummaryMetrics.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#samtools_flagstat/cram>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#insert_size_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_insert_size_metrics/insert_size_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#gc_bias_metrics_summary>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/gc_bias_metrics_summary> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl#gc_bias_metrics_chart>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "GcBiasMetricsChart.pdf" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#samtools_flagstat>
        cwl:in   <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#samtools_flagstat/cram> ;
        cwl:out  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#samtools_flagstat/flagstats> ;
        cwl:run  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/samtools_flagstat.cwl> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#reference>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/verify_bam_id.cwl#bam>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "--bam" ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/cram_to_bam.cwl#bam>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "output.bam" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_insert_size_metrics.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "collect insert size metrics" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/InsertSizeMetrics.txt" ]
                                   "H="
                                   [ cwl:valueFrom  "$(runtime.outdir)/InsertSizeHistogram.pdf" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_insert_size_metrics.cwl#metric_accumulation_level> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_insert_size_metrics.cwl#cram> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_insert_size_metrics.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_insert_size_metrics.cwl#insert_size_metrics> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  16000
                                 ] .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl#gc_bias_metrics_summary>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "GcBiasMetricsSummary.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_insert_size_metrics/metric_accumulation_level>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#picard_metric_accumulation_level> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_insert_size_metrics/cram>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_alignment_summary_metrics.cwl#cram>
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "INPUT=" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#gc_bias_metrics>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/gc_bias_metrics> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl#cram>
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/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/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_alignment_summary_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#reference> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_wgs_metrics>
        cwl:in   <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_wgs_metrics/intervals> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_wgs_metrics/cram> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_wgs_metrics/reference> ;
        cwl:out  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_wgs_metrics/wgs_metrics> ;
        cwl:run  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_wgs_metrics.cwl> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl#gc_bias_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "GcBiasMetrics.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/samtools_flagstat.cwl#flagstats>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "flagstat.out" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/verify_bam_id.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "verify BAM ID" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "--out"
                                   [ cwl:valueFrom  "$(runtime.outdir)/VerifyBamId" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/local/bin/verifyBamID" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/verify_bam_id.cwl#bam> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/verify_bam_id.cwl#vcf> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/verify_bam_id.cwl#verify_bam_id_metrics> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/verify_bam_id.cwl#verify_bam_id_depth> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  4000
                                 ] .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#omni_vcf>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#cram>
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#picard_metric_accumulation_level>
        cwl:default  "ALL_READS" ;
        sld:type     xsd:string , sld:null .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl>
        a                        cwl:Workflow ;
        rdfs:label               "cram_to_bam workflow" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#index_bam> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#cram_to_bam> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#cram> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#reference> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#bam> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_gc_bias_metrics.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "R=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_alignment_summary_metrics.cwl#reference>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "REFERENCE_SEQUENCE=" ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#index_bam/bam>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/cram_to_bam/workflow.cwl#cram_to_bam/bam> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_wgs_metrics/intervals>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#intervals> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_insert_size_metrics.cwl#cram>
        cwl:inputBinding    [ CommandLineBinding:prefix
                          "I=" ] ;
        cwl:secondaryFiles  []  ;
        sld:type            cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_wgs_metrics.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "collect WGS metrics" ;
        ns1:original_cwlVersion  "v1.0" ;
        cwl:arguments            ( "O="
                                   [ cwl:valueFrom  "$(runtime.outdir)/WgsMetrics.txt" ]
                                 ) ;
        cwl:baseCommand          ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectWgsMetrics" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_wgs_metrics.cwl#reference> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_wgs_metrics.cwl#intervals> , <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_wgs_metrics.cwl#cram> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_wgs_metrics.cwl#wgs_metrics> ;
        cwl:requirements         [ a                           cwl:ResourceRequirement ;
                                   ResourceRequirement:ramMin  16000
                                 ] .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_insert_size_metrics.cwl#insert_size_metrics>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "InsertSizeMetrics.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_insert_size_metrics/reference>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#reference> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_alignment_summary_metrics/cram>
        cwl:source  <https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram> .

<https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/collect_alignment_summary_metrics.cwl#metric_accumulation_level>
        cwl:inputBinding  [ CommandLineBinding:prefix
                          "METRIC_ACCUMULATION_LEVEL=" ] ;
        sld:type          xsd:string .