@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:source . cwl:source . 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.0" ] ; 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/fp_filter-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:source . sld:type xsd:string . a cwl:Workflow ; rdfs:label "varscan somatic 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:source . sld:type xsd:int , sld:null . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--variant:varscan" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . cwl:default false ; sld:type xsd:boolean , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--max_alt_allele_in_normal_fraction" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.hc.vcf" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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 "CombineVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-genotypeMergeOptions" "PRIORITIZE" "--rod_priority_list" "mutect,varscan,strelka,pindel" "-o" [ cwl:valueFrom "$(runtime.outdir)/combined.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:default "select_variants" ; sld:type xsd:string , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample)_bam_readcount_snv.tsv" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample)_bam_readcount_snv.tsv" ] ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:default "DNA" . cwl:source . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant:mutect" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type xsd:float , sld:null . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:valueFrom "strelka" . cwl:source . sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:default "Consequence" , "Feature" , "SYMBOL" , "HGVSp" , "HGVSc" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--dir" ] ; sld:type xsd:string . a cwl:Workflow ; rdfs:label "Apply filters to VCF file" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:source ; cwl:valueFrom "$(self)_filtered" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\n if (inputs.custom_gnomad_vcf) {\n return ['--check_existing', '--custom', inputs.custom_gnomad_vcf.path + ',gnomADe,vcf,exact,0,AF,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH,AF_SAS']\n }\n else {\n return []\n }\n}\n" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--synonyms" ] ; sld:type cwl:File , sld:null . cwl:in ; cwl:out ; cwl:run . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "annotated.vcf_summary.html" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "varscan v2.4.2 processSomatic" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(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 ; 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/cle:v1.3.1" ] ; 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/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File . cwl:source . cwl:in , , , , , ; cwl:out , ; cwl:run . 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:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "all_TD" ] ; sld:type cwl:File . sld:type xsd:string . cwl:default 400 ; sld:type xsd:int . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--assembly" ] ; sld:type xsd:string . sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "annotated.vcf" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . sld:type xsd:float , sld:null . cwl:source . sld:type xsd:boolean . 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 ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if(inputs.filter_docm_variants){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n" ] ; sld:type xsd:boolean . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "--max_alt_alleles_in_normal_count" ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self)_full" . cwl:source . cwl:source . 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:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . 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 400 ; sld:type xsd:int . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . 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:source . sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:float . cwl:in ; cwl:out ; cwl:run . cwl:default 5 ; sld:type xsd:float , sld:null . sld:type cwl:File , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default "NORMAL" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . 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:in ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "output.snp.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:outputSource ; cwl:secondaryFiles [] ; 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 ; 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I:tumor" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.vcf" ] ; sld:type cwl:File . cwl:default 8 ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string . 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; 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:source . cwl:source . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:in , , , , , , , , ; cwl:out , ; cwl:run . cwl:in , ; cwl:out ; cwl:run . sld:type xsd:string . sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default "indel" . 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:source . 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:in ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--coding_only" ] ; sld:type xsd:boolean . sld:type xsd:int . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:int . cwl:source . cwl:source . cwl:source . cwl:source . cwl:default "snv" . cwl:outputBinding [ CommandOutputBinding:glob "combined.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type cwl:File , sld:null . 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" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:default "merged" ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position -5 ] ; cwl:inputBinding [ CommandLineBinding:position -5 ] ; sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "pindel.out.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "all_chromosome_pindel.head" ] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample)_bam_readcount_indel.tsv" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample)_bam_readcount_indel.tsv" ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "Per-chromosome 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:default 1.5e-01 ; sld:type xsd:float , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . 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:ramMin 64000 ; ResourceRequirement:tmpdirMin 100000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:source . 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:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:xenial" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "all_chromosome_pindel.head" . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "pindel.noend.vcf.gz" ] ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:in , , , , ; cwl:out , , , , ; cwl:run . cwl:source . cwl:source . sld:type xsd:float . 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:outputBinding [ CommandOutputBinding:glob "results/variants/somatic.indels.vcf.gz" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "-PON" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default "NORMAL" . cwl:source . a cwl:Workflow ; rdfs:label "Varscan Workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "all_INV" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--variant:docm" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:default 0 ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:int , sld:null . 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 "$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/python" "/usr/bin/bam_readcount_helper.py" ) ; cwl:baseCommand ( "/usr/bin/python" "/usr/bin/bam_readcount_helper.py" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam_readcount_helper-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam_readcount_helper-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.sample)_bam_readcount.tsv" . cwl:source . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--minimum_depth" ] ; sld:type xsd:int . 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 "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . cwl:in ; cwl:out ; cwl:run . cwl:default 400 ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:position -4 ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position -3 ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "per_chromosome_pindel.out" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:default true . sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type xsd:float , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . 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: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:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--cosmic" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . 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: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:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl: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 ; 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; 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: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: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: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 "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:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.file.basename).gz" . cwl:default 1 ; sld:type xsd:int , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "mutect.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default "TUMOR" . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somatic.snvs.vcf.gz" ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "fp_filter workflow" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , ; 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 ; NetworkAccess:networkAccess true ] ; 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "interval_list.bed" ] ; sld:type cwl:File . sld:type xsd:string . 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 "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . 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 ; 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 "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: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:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . 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:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "variants.annotated.tsv" ] ; sld:type cwl:File . 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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:xenial" ] ; cwl:stdout "per_chromosome_pindel.out" . cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "output.indel.vcf" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--tumorBam=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "bash" "-c" "/bin/grep -v '^@' $1 | /usr/bin/cut -f 1 | /usr/bin/sort | /usr/bin/uniq" "--" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:xenial" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "chromosome.list" . cwl:source . cwl:default "TUMOR" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Filter variants from the DoCM detector" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(runtime.outdir)/docm_filtered_variants.vcf" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/docm_filter.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:v1.4.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . 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:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(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 . cwl:source . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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 4 ; CommandLineBinding:prefix "--alleles" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-f" ] ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "somatic_llr_filtered.vcf" ] ; sld:type cwl:File . cwl:source . 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:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--artifact_detection_mode" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "merged.vcf.gz" ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "depth_filtered.vcf" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . 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 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "docm_filtered_variants.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -7 ] ; cwl:inputBinding [ CommandLineBinding:position -7 ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "all_LI" ] ; sld:type cwl:File . cwl:source . rdfs:comment "Used to explicitly define which assembly version to use; required when there are two or more in the same directory" ; sld:type xsd:string . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . 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" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "add_gt.vcf" ] ; sld:type cwl:File . cwl:source . cwl:valueFrom "pindel" . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.hc.vcf" ] ; sld:type cwl:File . cwl:source . 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:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default 9.9e-01 ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; sld:type xsd:float , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type xsd:float . cwl:source , . cwl:source . cwl:valueFrom "mutect" . cwl:source . cwl:source . sld:type xsd:string . 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: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:baseCommand ( "vt" "decompose" ) ; 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 ; 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 ; 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 "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: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: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:outputSource ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:position -2 ] ; cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:default "DNA" . cwl:source . cwl:source . cwl:in , , , , , ; cwl:out ; cwl:run . 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 ; 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: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:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:outputBinding [ CommandOutputBinding:glob "all_D" ] ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:in , , , ; cwl:out , ; cwl:run . a cwl:Workflow ; rdfs:label "process VCF 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 . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type cwl:File , sld:null . 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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , , , , ; cwl:out ; cwl:run . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 8 ; sld:type xsd:int , sld:null . sld:type cwl:File . cwl:in , ; cwl:out , , , , , ; cwl:run . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "mapq_filtered.vcf.gz" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:source . cwl:in , , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:source . 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:source . 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 . 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:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "SCATTER_COUNT=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . 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 "$(runtime.outdir)/mapq_filtered.vcf.gz" ] ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mapq0-filter:v0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ; ResourceRequirement:tmpdirMin 10000 ] . cwl:default "AD" , "GT" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(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: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 [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "annotated.af_filtered.vcf" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . sld:type xsd:float . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "mutect2 (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/mutect.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "MuTect2" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 20000 ; ResourceRequirement:tmpdirMin 100000 ] . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--variant:pindel" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "all_SI" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 9 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--plugin" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "add GT tags" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/bin/perl" "/usr/bin/add_strelka_gt.pl" "$(inputs.vcf.path)" "$(runtime.outdir)" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position -6 ] ; cwl:inputBinding [ CommandLineBinding:position -6 ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:default "TUMOR" . sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:source . cwl:in , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "add VEP annotation to report" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/variants.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" ] . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:string . cwl:source , , , , . cwl:source . sld:type xsd:int , 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 . 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 ; 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 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantsToTable" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--variant:strelka" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "pindel parallel workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -4 ] ; cwl:inputBinding [ CommandLineBinding:position -4 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "gnomADe_AF filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(inputs.vcf.path)" ] [ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ] "/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/vcf_check.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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:1.0.0" ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--exome" ] ; sld:type xsd:boolean . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type xsd:int , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.hc.vcf" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/intervals_to_bed.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/perl_helper-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "interval_list.bed" . cwl:source . cwl:default "HGVSp" , "HGVSc" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "CombineVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-genotypeMergeOptions" "PRIORITIZE" "--rod_priority_list" "callers,docm" "--setKey" "null" "-o" [ cwl:valueFrom "$(runtime.outdir)/merged.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:source . cwl:source , . cwl:source . cwl:source . cwl:source . sld:type xsd:boolean . cwl:source . cwl:default "Wildtype" , "Downstream" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:default true ; sld:type xsd:boolean , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(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:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . cwl:in , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . 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:outputBinding [ CommandOutputBinding:glob "output.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "output.vcf.gz" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-c" ] ; sld:type xsd:string . 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" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . 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" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . sld:type cwl:File , sld:null . cwl:source . cwl:default 1e-01 ; sld:type xsd:float , sld:null . 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:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--dbsnp" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "annotated_filtered.vcf" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type xsd:float , sld:null . 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:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:valueFrom "varscan" . cwl:default "ID" , "ALT" , "set" , "AC" , "CHROM" , "POS" , "REF" , "AF" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; cwl:valueFrom "${\n return [\n \"--filter\",\n [\n \"gnomADe_AF\", \"<\", inputs.maximum_population_allele_frequency,\n \"or not\", \"gnomADe_AF\"\n ].join(\" \")\n ]\n}\n" ] ; sld:type xsd:float . cwl:in , , , ; cwl:out , ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:boolean . a cwl:Workflow ; rdfs:label "Detect Docm variants" ; 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 ] . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -2 ; CommandLineBinding:prefix "--llr-threshold" ] ; sld:type xsd:float . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . 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" "--everything" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 64000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:1.1.0" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . a cwl:CommandLineTool ; rdfs:label "varscan v2.4.2 somatic" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/bin/varscan_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 12000 ] . cwl:source . sld:type xsd:string . cwl:default 400 ; sld:type xsd:int . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . cwl:default "fpfilter" ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "cle_annotated_vcf_filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(inputs.vcf.path)" "$(runtime.outdir)" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/docm_and_coding_indel_selection.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:string . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant:callers" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "vcf index" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(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:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; 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 ; 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 ; 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: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 ; 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:inputs ; cwl:outputs ; 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: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:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; 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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; 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: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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; 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: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:ShellCommandRequirement ] ; 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: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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; 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: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: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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; 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:ShellCommandRequirement ] ; 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: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: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:source . cwl:source . 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/strelka-cwl:2.9.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 4000 ] . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run . a cwl:Workflow ; rdfs:label "Detect Variants 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:source . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--referenceFasta=" ; CommandLineBinding:separate false ] ; sld:type xsd:string . 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:in , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "HaplotypeCaller (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-gt_mode" "GENOTYPE_GIVEN_ALLELES" "-o" [ cwl:valueFrom "$(runtime.outdir)/docm_raw_variants.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "HaplotypeCaller" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . cwl:source . sld:type xsd:boolean . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(runtime.outdir)/$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(runtime.outdir)/$(self.basename)" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; 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 ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "filter" ] ; sld:type xsd:boolean . 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:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*.interval_list" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . 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" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; sld:type xsd:boolean , sld:null . cwl:in , , , , , , , , ; cwl:out , , , ; cwl:run . cwl:default 1e-01 ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "docm_raw_variants.vcf" ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . 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 ; 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/somatic-llr-filter:v0.3" ] . cwl:outputBinding [ CommandOutputBinding:glob "chromosome.list" ; CommandOutputBinding:outputEval "$( self[0].contents.split(\"\\n\").slice(0, -1))" ; cwl:loadContents true ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:in , ; cwl:out , , , , , ; cwl:run . cwl:source . cwl:in , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Normalize variants" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(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 ; 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; 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:source . cwl:in ; cwl:out ; cwl:run . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:source . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:default "NORMAL,TUMOR" . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . 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:source . cwl:default 1e-03 ; sld:type xsd:float , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:default 1e-01 ; cwl:inputBinding [ CommandLineBinding:position 6 ] ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-I:normal" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . 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)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(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:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; 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: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: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: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: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:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source .