@prefix LoadListingRequirement: . @prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix cwl: . @prefix ResourceRequirement: . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "fp_filter workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type xsd:string . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:default 2 ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext.equals(\".gz\")){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "bgzip and index VCF" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 0 ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:label "varscan v2.4.2 germline" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 9 ; cwl:valueFrom "$(runtime.outdir)/output.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/varscan_germline_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 12000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/varscan_helper-cwl:1.0.0" ] . cwl:default 1e-01 ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:default 2 ; cwl:inputBinding [ CommandLineBinding:position 6 ] ; sld:type xsd:int , sld:null . cwl:source . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:valueFrom "varscan" . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string . cwl:default 5e-02 ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; sld:type xsd:float , sld:null . sld:type xsd:string . cwl:source . cwl:source ; cwl:valueFrom "$(self)_filtered" . a cwl:CommandLineTool ; rdfs:label "run vt decompose" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . a cwl:CommandLineTool ; rdfs:label "bgzip VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:stdout "$(inputs.file.basename).gz" . cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:default "fpfilter" ; sld:type xsd:string , sld:null . rdfs:comment "include genotypes from this sample" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:default 1e-01 ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:float , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "interval_list.bed" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 10 ] ; sld:type cwl:File , sld:null . cwl:source . cwl:default "select_variants" ; sld:type xsd:string , sld:null . cwl:in , , , ; cwl:out ; cwl:run . cwl:default 8 ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:int , sld:null . cwl:in , , , , , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/intervals_to_bed.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/perl_helper-cwl:1.0.0" ] ; cwl:stdout "interval_list.bed" . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Normalize variants" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 8 ; sld:type xsd:int , sld:null . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "output.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; sld:type cwl:File . cwl:default true . a cwl:Workflow ; rdfs:label "Varscan Workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source ; cwl:valueFrom "$(self)_full" . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default 9.9e-01 ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "TUMOR" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; sld:type xsd:string , sld:null . 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 ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:source . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "vcf index" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "False Positive filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . a cwl:CommandLineTool ; rdfs:label "Sanitize a VCF" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\ntabix -p vcf $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] . sld:type xsd:string . cwl:source . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null .