@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:default "Consequence" , "Feature" , "SYMBOL" , "HGVSp" , "HGVSc" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . cwl:default "indel" . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:default "variants" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "create filtered VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--maskName" "processSomatic" "--filterNotInMask" "-o" [ cwl:valueFrom "$(runtime.outdir)/output.vcf.gz" ] ) ; cwl:arguments ( "--maskName" "processSomatic" "--filterNotInMask" "-o" [ cwl:valueFrom "$(runtime.outdir)/output.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantFiltration" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantFiltration" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:in , , , ; cwl:out ; cwl:run . sld:type xsd:string . a cwl:Workflow ; rdfs:label "Per-region pindel" ; 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:MultipleInputFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default "NORMAL,TUMOR" . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "annotated_filtered.vcf" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "SCATTER_COUNT=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somatic.indels.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:in , , , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , , , , ; cwl:out , , , , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "SCATTER_COUNT=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:position -2 ] ; cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type cwl:File . cwl:in , ; cwl:out , , , , , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--normalBam=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant:mutect" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "varscan v2.4.2 processSomatic" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(inputs.variants.path)" "$(runtime.outdir)/$(inputs.variants.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "java" "-jar" "/opt/varscan/VarScan.jar" "processSomatic" ) ; cwl:arguments ( "cp" "$(inputs.variants.path)" "$(runtime.outdir)/$(inputs.variants.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "java" "-jar" "/opt/varscan/VarScan.jar" "processSomatic" ) ; cwl:cwlVersion ; 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:inputs , ; cwl:outputs , , , , , ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "add_gt.vcf" ] ; sld:type cwl:File . cwl:in , , , , , , , , ; cwl:out , , , ; cwl:run . cwl:source . a cwl:CommandLineTool ; rdfs:label "Mutect2 (GATK 4)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "mutect.vcf.gz" ] ) ; cwl:baseCommand ( "/bin/bash" "Mutect2.sh" ) ; 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 "broadinstitute/gatk:4.1.2.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 32000 ; ResourceRequirement:tmpdirMin 100000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\nTUMOR=`(samtools view -H $3 | grep \"^@RG\" | sed \"s/.*SM:\\([^\\t]*\\).*/\\1/g\" | head -n 1)` #Extracting the sample name from the TUMOR bam.\nNORMAL=`(samtools view -H $4 | grep \"^@RG\" | sed \"s/.*SM:\\([^\\t]*\\).*/\\1/g\" | head -n 1)` #Extracting the sample name from the NORMAL bam.\n/gatk/gatk Mutect2 --java-options \"-Xmx20g\" -O $1 -R $2 -I $3 -tumor $TUMOR -I $4 -normal $NORMAL -L $5 #Running Mutect2.\ngunzip mutect.vcf.gz #Unzipping the Mutect2 output vcf file to alter the header names.\ngrep \"^##\" mutect.vcf >mutect.final.vcf #Extracting all the lines above #CHROM in the vcf to a new output vcf.\ngrep \"^#CHROM\" mutect.vcf | sed \"s/\\<$TUMOR\\>/TUMOR/g; s/\\<$NORMAL\\>/NORMAL/g\" >> mutect.final.vcf #Concatenating the #CHROM line with substituted sample headers to the output vcf.\nperl -nae 'print $_ unless $_ =~ /^#/' mutect.vcf >> mutect.final.vcf #Concatenating the sites to the output vcf. Changed grep to perl because grep throws a rc of 1 if the output is null.\nbgzip mutect.final.vcf #Bzipping the final output vcf.\ntabix mutect.final.vcf.gz #Indexing the bzipped output vcf.\nmv mutect.vcf.gz.stats mutect.final.vcf.gz.stats #Renaming the .stats file to match the name conversion of the final output vcf.\n/gatk/gatk FilterMutectCalls -R $2 -V mutect.final.vcf.gz -O mutect.final.filtered.vcf.gz #Running FilterMutectCalls on the output vcf.\n" ; cwl:entryname "Mutect2.sh" ] ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:default 9.9e-01 ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; sld:type xsd:float , sld:null . sld:type xsd:int , sld:null . sld:type cwl:File . cwl:default "Wildtype" , "Downstream" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in , ; cwl:out ; cwl:run . cwl:in , , , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source , , , , . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "ALT" , "REF" , "AC" , "AF" , "ID" , "set" , "POS" , "CHROM" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type cwl:File , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -7 ] ; cwl:inputBinding [ CommandLineBinding:position -7 ] ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "remove END INFO tags" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-x" "INFO/END" "-Oz" "-o" [ cwl:valueFrom "$(runtime.outdir)/pindel.noend.vcf.gz" ] ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "annotate" ) ; 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/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . cwl:source . sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--referenceFasta=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . sld:type xsd:int . 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 "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; 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 "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; 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 "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; 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 "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; sld:type cwl:File . sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--tumorBam=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "flag_pick" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--" ; CommandLineBinding:separate false ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . sld:type cwl:File . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--dir" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string . sld:type cwl:File . cwl:default 400 ; sld:type xsd:int . cwl:source . sld:type cwl:File , sld:null . sld:type xsd:boolean , sld:null . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "per_chromosome_pindel.out" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default 400 ; sld:type xsd:int . cwl:default 8 ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:int , sld:null . sld:type xsd:float , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:source . a cwl:Workflow ; rdfs:label "mutect parallel 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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "bgzip and index VCF" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion ; 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs . sld:type cwl:File . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position -8 ] ; cwl:inputBinding [ CommandLineBinding:position -8 ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.hc.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:float . cwl:source . cwl:in , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/bin/grep" "ChrID" "/dev/stdin" ) ; cwl:baseCommand ( "/bin/cat" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:xenial" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "all_region_pindel.head" . cwl:outputBinding [ CommandOutputBinding:glob "pindel.out.vcf" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "CombineVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-genotypeMergeOptions" "PRIORITIZE" "--rod_priority_list" "mutect,varscan,strelka,pindel" "-o" [ cwl:valueFrom "$(runtime.outdir)/combined.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ; 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/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:source . sld:type xsd:float . cwl:outputBinding [ CommandOutputBinding:glob "depth_filtered.vcf" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "all_D" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--minimum_depth" ] ; sld:type xsd:int . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--variant:strelka" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; sld:type cwl:File . cwl:source . sld:type xsd:float , sld:null . cwl:source . sld:type xsd:boolean . cwl:in , , , ; cwl:out , ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type xsd:string , sld:null . cwl:source . cwl:valueFrom "pindel" . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.vcf" ] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:valueFrom "mutect" . a cwl:CommandLineTool ; rdfs:label "varscan v2.4.2 somatic" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/bin/varscan_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:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 12000 ] . cwl:default "fpfilter" ; sld:type xsd:string , sld:null . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "filter vcf for variants with high percentage of mapq0 reads" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/bin/bash" "/usr/bin/mapq0_vcf_filter.sh" [ cwl:valueFrom "$(runtime.outdir)/mapq_filtered.vcf.gz" ] ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ; ResourceRequirement:tmpdirMin 10000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mapq0-filter:v0.3.1" ] . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . cwl:source . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "output.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "output.vcf.gz" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "OUTPUT=$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/split_interval_list_helper.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/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ] . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "run vt decompose" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; 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: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:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--synonyms" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:default "NORMAL" . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:valueFrom "annotated_filtered.vcf" . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:default 400 ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "mapq_filtered.vcf.gz" ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/bin/cat" ) ; 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 "ubuntu:xenial" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "per_chromosome_pindel.out" . cwl:source . a cwl:Workflow ; rdfs:label "Apply filters to VCF file" ; 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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "all_SI" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "add GT tags" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/bin/perl" "/usr/bin/add_strelka_gt.pl" "$(inputs.vcf.path)" "$(runtime.outdir)" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "vcf merge" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ] ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputSource ; sld:type cwl:File . sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "add bam_readcount info to vcf" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--everything" ] ; sld:type xsd:boolean , sld:null . sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--allowMissingData" "-o" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantsToTable" ) ; 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 ] . sld:type cwl:File . cwl:source . sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/intervals_to_bed.pl" ) ; 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 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/perl_helper-cwl:1.0.0" ] ; cwl:stdout "interval_list.bed" . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.hc.vcf" ] ; sld:type cwl:File . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:source . cwl:default "ID" , "ALT" , "CHROM" , "POS" , "REF" , "set" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:default "NOPREFIX" ; cwl:inputBinding [ CommandLineBinding:position -4 ] ; cwl:inputBinding [ CommandLineBinding:position -4 ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position -5 ] ; cwl:inputBinding [ CommandLineBinding:position -5 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default false ; sld:type xsd:boolean , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "TUMOR" . a cwl:Workflow ; rdfs:label "Varscan 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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "run bam-readcount" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position -3 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:arguments ( [ CommandLineBinding:position -3 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/python" "/usr/bin/bam_readcount_helper.py" ) ; cwl:baseCommand ( "/usr/bin/python" "/usr/bin/bam_readcount_helper.py" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam_readcount_helper-cwl:1.1.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam_readcount_helper-cwl:1.1.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] ; cwl:stdout "$(inputs.sample)_bam_readcount.tsv" . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "output.indel.vcf" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-j" ] ; sld:type cwl:File , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "filter variants at sites below a given sequence depth in each sample" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(runtime.outdir)/depth_filtered.vcf" ] ) ; cwl:baseCommand ( "/opt/conda/bin/python3" "/usr/bin/depth_filter.py" ) ; 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/depth-filter:0.1.2" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . sld:type xsd:float , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:source . cwl:source . rdfs:comment "include genotypes from this sample" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run . cwl:source ; cwl:valueFrom "$(self)_filtered" . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 1e-01 ; cwl:inputBinding [ CommandLineBinding:position 6 ] ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-c" ] ; sld:type xsd:string , sld:null . cwl:default "DNA" . cwl:source . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 9 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--plugin" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:default "TUMOR" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "filter" ] ; sld:type xsd:boolean . cwl:outputBinding [ CommandOutputBinding:glob "*.interval.bed" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "all_LI" ] ; sld:type cwl:File . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:default "DNA" . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type xsd:string . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--variant:varscan" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; sld:type cwl:File . sld:type xsd:string . a cwl:CommandLineTool ; rdfs:comment "Renames a file by staging and then `mv`ing it. A workaround for workflow engines that don't support rename.cwl. If running in cwltool, use the other one instead." ; rdfs:label "Staged Renamer" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] . cwl:outputBinding [ CommandOutputBinding:glob "annotated.vcf_summary.html" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "cle_annotated_vcf_filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(inputs.vcf.path)" "$(runtime.outdir)" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/docm_and_coding_indel_selection.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . cwl:default 0 ; sld:type xsd:int , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:default "AD" , "AF" , "DP" , "GT" ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GF" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--exome" ] ; sld:type xsd:boolean . sld:type xsd:boolean . cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext.equals(\".gz\")){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext.equals(\".gz\")){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext.equals(\".gz\")){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext.equals(\".gz\")){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type cwl:File . cwl:default 1e-01 ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--max-normal-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--max-normal-freq" ] ; sld:type xsd:float , sld:null . cwl:source , . cwl:default 1e-01 ; sld:type xsd:float , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; sld:type cwl:File . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "all_INV" ] ; sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:default 400 ; sld:type xsd:int . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:default true . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "bgzip VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; 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: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: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: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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl: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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.file.basename).gz" . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:source . cwl:source . a cwl:Workflow ; rdfs:label "process VCF workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs . cwl:outputBinding [ CommandOutputBinding:glob "output.snp.vcf" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "all_region_pindel.head" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 1 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . a cwl:Workflow ; rdfs:label "fp_filter workflow" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:position 7 ; cwl:valueFrom "${\n if (inputs.custom_clinvar_vcf) {\n return [\"--custom\", inputs.custom_clinvar_vcf.path + \",clinvar,vcf,exact,0,CLINSIGN,PHENOTYPE,SCORE,RCVACC,TESTEDINGTR,PHENOTYPELIST,NUMSUBMIT,GUIDELINES\"]\n\n }\n else {\n return []\n }\n}\n" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "OUTPUT=$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/split_interval_list_to_bed_helper.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/cle:v1.4.2" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ] . cwl:in ; cwl:out ; cwl:run . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: 'homo_sapiens' or 'mus_musculus'" ; cwl:inputBinding [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "--species" ] ; sld:type xsd:string . cwl:source . cwl:default 50 ; sld:type xsd:int . sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . rdfs:comment "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "--assembly" ] ; sld:type xsd:string . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -2 ; CommandLineBinding:prefix "--llr-threshold" ] ; sld:type xsd:float . cwl:source . cwl:default 1.5e-01 ; sld:type xsd:float , sld:null . cwl:in , ; cwl:out , , , , , ; cwl:run . cwl:in , , , , , ; cwl:out , ; cwl:run . a cwl:Workflow ; rdfs:label "varscan somatic 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:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "Sanitize a VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; 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:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; 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: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: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: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 $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] . cwl:source . a cwl:Workflow ; rdfs:label "Detect Variants workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , , , , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "vcf index" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(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: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)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(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: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)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(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: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)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(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: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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; 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:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; 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: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:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; 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:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; 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:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; 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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; 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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; 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: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:requirements [ a cwl:ShellCommandRequirement ] ; 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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; 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: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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; 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: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: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: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: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:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--variant:pindel" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "add VEP annotation to report" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ] ) ; cwl:baseCommand ( "vep-annotation-reporter" ) ; 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 "griffithlab/vatools:3.1.0" ] . a cwl:Workflow ; rdfs:label "Add snv and indel bam-readcount files to a vcf" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion ; 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:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\n if (inputs.custom_gnomad_vcf) {\n return ['--check_existing', '--custom', inputs.custom_gnomad_vcf.path + ',gnomADe,vcf,exact,0,AF,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH,AF_SAS']\n }\n else {\n return []\n }\n}\n" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:in , , , , ; cwl:out ; cwl:run . sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "*.interval_list" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.vcf" ] ; sld:type cwl:File . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--coding_only" ] ; sld:type xsd:boolean . cwl:outputBinding [ CommandOutputBinding:glob "somatic_llr_filtered.vcf" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "combined.vcf.gz" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "pindel v0.2.5b8" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/bin/perl" "/usr/bin/pindel_helper.pl" "$(inputs.normal_bam.path)" "$(inputs.tumor_bam.path)" "$(inputs.insert_size)" ) ; 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:coresMin 4 ; ResourceRequirement:ramMin 16000 ; ResourceRequirement:tmpdirMin 100000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.4.2" ] . rdfs:comment "ensembl version - Must be present in the cache directory. Example: '95'" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "--cache_version" ] ; sld:type xsd:string . cwl:default "AD" , "GT" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_indel.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_indel.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; sld:type cwl:File . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(runtime.outdir)/$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(runtime.outdir)/$(self.basename)" ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . cwl:default "merged" ; sld:type xsd:string , sld:null . sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -6 ] ; cwl:inputBinding [ CommandLineBinding:position -6 ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-f" ] ; sld:type xsd:string . sld:type cwl:File , sld:null . sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; sld:type xsd:boolean , sld:null . cwl:in , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 5 ; sld:type xsd:float , sld:null . cwl:default "snv" . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somatic.snvs.vcf.gz" ] ; sld:type cwl:File . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Normalize variants" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ; 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; 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:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.hc.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:default "select_variants" ; sld:type xsd:string , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "pindel.noend.vcf.gz" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_snv.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_snv.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:default "TUMOR" . cwl:source . cwl:source . cwl:source . cwl:in , , , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:valueFrom "strelka" . a cwl:CommandLineTool ; rdfs:label "False Positive filter" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:cwlVersion ; 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 ; 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:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; 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 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . sld:type xsd:float . cwl:source . cwl:default 5e-02 ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; sld:type xsd:float , sld:null . cwl:default 0 ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:int , sld:null . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "strelka 2.9.9" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "$(inputs.cpu_reserved)" ] [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/docker_helper.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/strelka-cwl:2.9.9" ] . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "pindel somatic filter v1" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/bin/perl" "/usr/bin/write_pindel_filter_config.pl" "$(inputs.pindel_output_summary.path)" "$(inputs.reference)" "$(runtime.outdir)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/perl" "/usr/bin/somatic_indelfilter.pl" "filter.config" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] . cwl:outputBinding [ CommandOutputBinding:glob "all_TD" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "Ensembl Variant Effect Predictor" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--format" "vcf" "--vcf" "--fork" "4" "--term" "SO" "--transcript_version" "--offline" "--cache" "--symbol" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ; 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:coresMin 4 ; ResourceRequirement:ramMin 64000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:1.1.0" ] . a cwl:Workflow ; rdfs:label "pindel parallel 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:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "annotated.vcf" ] ; sld:type cwl:File . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--mask" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--mask" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; 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:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; 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:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "$(self)_full" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "interval_list.bed" ] ; sld:type cwl:File . cwl:in , , , , , , , , ; cwl:out , ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:default 0 ; cwl:inputBinding [ CommandLineBinding:position -1 ] ; cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:type cwl:File . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "mutect.final.filtered.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; sld:type cwl:File . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:in ; cwl:out ; cwl:run . a cwl:Workflow ; rdfs:label "strelka 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:source , . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:valueFrom "varscan" . a cwl:CommandLineTool ; rdfs:label "use the binomial/llr somatic filter to weed out low confidence variants" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--overwrite" [ cwl:valueFrom "$(runtime.outdir)/somatic_llr_filtered.vcf" ] ) ; cwl:baseCommand ( "/opt/conda/bin/python3" "/usr/bin/somatic_llr_filter.py" ) ; 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/somatic-llr-filter:v0.4.3" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "NORMAL" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source .