@prefix LoadListingRequirement: . @prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix ScatterMethod: . @prefix cwl: . @prefix ResourceRequirement: . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "*.pass.bcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.pass.bcf" ] ; cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "Alias for -d none" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--remove-duplicates" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--remove-duplicates" ] ; sld:type xsd:boolean , sld:null . sld:type cwl:File . rdfs:comment "Do not output PS tag at each site, only at the start of a new phase set block." ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--compact-PS" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--compact-PS" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . rdfs:comment "VEPs base cache/plugin directory" ; cwl:inputBinding [ CommandLineBinding:prefix "--vep-data" ] ; sld:type xsd:string , sld:null . rdfs:comment "min. coverage in tumor" ; cwl:default 10 ; cwl:inputBinding [ CommandLineBinding:prefix "--coverage" ] ; sld:type xsd:int , sld:null . sld:type xsd:string . cwl:source . sld:type cwl:File . cwl:source . rdfs:comment "min. mapping quality for genotyping" ; cwl:default 5 ; cwl:inputBinding [ CommandLineBinding:prefix "--geno-qual" ] ; sld:type xsd:int , sld:null . rdfs:comment "Number of forked processes to use when running VEP" ; cwl:default 4 ; cwl:inputBinding [ CommandLineBinding:prefix "--vep-forks" ] ; sld:type xsd:int , sld:null . rdfs:comment "The non-TCGA VCF from exac.broadinstitute.org" ; cwl:inputBinding [ CommandLineBinding:prefix "--filter-vcf" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . rdfs:comment " Number of extra output compression threads [0]" ; cwl:inputBinding [ CommandLineBinding:prefix "--threads" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--threads" ] ; sld:type xsd:string , sld:null . cwl:valueFrom "${ return inputs.tumor_sample_name + \".\" + inputs.normal_sample_name +\".\" + inputs.t + \".bcf\"; }" . rdfs:comment "Filter mode (somatic, germline)" ; cwl:default "somatic" ; cwl:inputBinding [ CommandLineBinding:prefix "--filter" ] ; sld:type xsd:string , sld:null . rdfs:comment "min. median GQ for carriers and non-carriers" ; cwl:default 15 ; cwl:inputBinding [ CommandLineBinding:prefix "--gq" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . rdfs:comment "Matched_Norm_Sample_Barcode to report in the MAF" ; cwl:default "NORMAL" ; cwl:inputBinding [ CommandLineBinding:prefix "--normal-id" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in , , , , ; cwl:out ; cwl:run . cwl:valueFrom "${ return \"86\"; }" . rdfs:comment "include regions marked in this genome" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--all_regions" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "First coordinate of the next file can precede last record of the current file." ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--allow-overlaps" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--allow-overlaps" ] ; sld:type xsd:boolean , sld:null . rdfs:comment " Break phase set if phasing quality is lower than [30]" ; cwl:inputBinding [ CommandLineBinding:prefix "--min-PQ" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--min-PQ" ] ; sld:type xsd:string , sld:null . rdfs:comment "min. fractional ALT support" ; cwl:default 4e-02 ; cwl:inputBinding [ CommandLineBinding:prefix "--altaf" ] ; sld:type xsd:float , sld:null . cwl:source . a cwl:CommandLineTool ; cwl:arguments ( "awk" "-F" "\t" "NR==1 { for(i=1;i<=NF;i++){ f[$i]=i } } { print \\$(f[\"Hugo_Symbol\"])\"\\\\t\"\\$(f[\"Entrez_Gene_Id\"])\"\\\\t\"\\$(f[\"Center\"])\"\\\\t\"\\$(f[\"Tumor_Sample_Barcode\"])\"\\\\t\"\\$(f[\"Fusion\"])\"\\\\t\"\\$(f[\"DNA_support\"])\"\\\\t\"\\$(f[\"RNA_support\"])\"\\\\t\"\\$(f[\"Method\"])\"\\\\t\"\\$(f[\"Frame\"])}" ) ; cwl:arguments ( "awk" "-F" "\t" "NR==1 { for(i=1;i<=NF;i++){ f[$i]=i } } { print \\$(f[\"Hugo_Symbol\"])\"\\\\t\"\\$(f[\"Entrez_Gene_Id\"])\"\\\\t\"\\$(f[\"Center\"])\"\\\\t\"\\$(f[\"Tumor_Sample_Barcode\"])\"\\\\t\"\\$(f[\"Fusion\"])\"\\\\t\"\\$(f[\"DNA_support\"])\"\\\\t\"\\$(f[\"RNA_support\"])\"\\\\t\"\\$(f[\"Method\"])\"\\\\t\"\\$(f[\"Frame\"])}" ) ; cwl:baseCommand () ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "alpine:3.8" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "alpine:3.8" ] ; cwl:stdout "$(inputs.output_filename)" . rdfs:comment "Species of variants in input" ; cwl:default "homo_sapiens" ; cwl:inputBinding [ CommandLineBinding:prefix "--species" ] ; sld:type xsd:string , sld:null . cwl:in ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . rdfs:comment "input VCF/BCF file for re-genotyping" ; cwl:inputBinding [ CommandLineBinding:prefix "--vcffile" ] ; sld:type xsd:string , sld:null . rdfs:comment "Comma-delimited names of FORMAT fields to retain as extra columns in MAF []" ; cwl:inputBinding [ CommandLineBinding:prefix "--retain-fmt" ] ; sld:type xsd:string , sld:null . cwl:in , , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; sld:type cwl:File . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.o)\n return inputs.o;\n return null;\n}\n" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "min. fraction of genotyped samples" ; cwl:default 0e+00 ; cwl:inputBinding [ CommandLineBinding:prefix "--ratiogeno" ] ; sld:type xsd:float , sld:null . cwl:source . sld:type xsd:string . cwl:valueFrom "${ return inputs.extracted_file.basename.replace(\".extracted.txt\", \".columns_added.txt\"); }" . cwl:source . rdfs:comment "Array of vcf files to be concatenated into one vcf" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Chain file to remap variants to a different assembly before running VEP" ; cwl:inputBinding [ CommandLineBinding:prefix "--remap-chain" ] ; sld:type xsd:string , sld:null . cwl:in , ; cwl:out ; cwl:run . cwl:in , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:valueFrom "${ return inputs.tumor_sample_name + \".\" + inputs.normal_sample_name + \".svs.vcf\"; }" . rdfs:comment "min. paired-end mapping quality" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "--map-qual" ] ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:comment "concatenate VCF/BCF files from the same set of samples\n" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/bin/bcftools" "concat" ) ; cwl:baseCommand ( "/usr/bin/bcftools" "concat" ) ; 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 "mskcc/roslin-variant-htslib:1.9" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mskcc/roslin-variant-htslib:1.9" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Folder containing variant_effect_predictor.pl or vep binary" ; cwl:inputBinding [ CommandLineBinding:prefix "--vep-path" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . rdfs:comment "min. SV size" ; cwl:default 500 ; cwl:inputBinding [ CommandLineBinding:prefix "--minsize" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "When reporting co-located variants, allow mismatched variant alleles too" ; cwl:inputBinding [ CommandLineBinding:prefix "--any-allele" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; cwl:arguments ( "awk" "-F" "\t" "NR==1 { for(i=1;i<=NF;i++){ f[$i]=i } print \"Hugo_Symbol\\\\tEntrez_Gene_Id\\\\tCenter\\\\tTumor_Sample_Barcode\\\\tFusion\\\\tMethod\\\\tFrame\" } NR>1 { print \\$(f[\"Hugo_Symbol\"])\"\\\\t\"\\$(f[\"Entrez_Gene_Id\"])\"\\\\t\"\\$(f[\"Center\"])\"\\\\t\"\\$(f[\"Tumor_Sample_Barcode\"])\"\\\\t\"\\$(f[\"Fusion\"])\"\\\\t\"\\$(f[\"Method\"])\"\\\\t\"\\$(f[\"Frame\"])}" ) ; cwl:arguments ( "awk" "-F" "\t" "NR==1 { for(i=1;i<=NF;i++){ f[$i]=i } print \"Hugo_Symbol\\\\tEntrez_Gene_Id\\\\tCenter\\\\tTumor_Sample_Barcode\\\\tFusion\\\\tMethod\\\\tFrame\" } NR>1 { print \\$(f[\"Hugo_Symbol\"])\"\\\\t\"\\$(f[\"Entrez_Gene_Id\"])\"\\\\t\"\\$(f[\"Center\"])\"\\\\t\"\\$(f[\"Tumor_Sample_Barcode\"])\"\\\\t\"\\$(f[\"Fusion\"])\"\\\\t\"\\$(f[\"Method\"])\"\\\\t\"\\$(f[\"Frame\"])}" ) ; cwl:baseCommand () ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "alpine:3.8" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "alpine:3.8" ] ; cwl:stdout "$(inputs.output_filename)" . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type cwl:File . rdfs:comment " Read the list of files from a file." ; cwl:inputBinding [ CommandLineBinding:prefix "--file-list" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--file-list" ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; sld:type cwl:File . rdfs:comment " b - compressed BCF, u - uncompressed BCF, z - compressed VCF, v - uncompressed VCF [v]" ; cwl:inputBinding [ CommandLineBinding:prefix "--output-type" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--output-type" ] ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment " Restrict to comma-separated list of regions" ; cwl:inputBinding [ CommandLineBinding:prefix "--regions" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--regions" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type xsd:string . rdfs:comment "log stderr to file" ; cwl:inputBinding [ CommandLineBinding:prefix "--stderr" ] ; sld:type xsd:string , sld:null . rdfs:comment "Path to input file in VCF format" ; cwl:inputBinding [ CommandLineBinding:prefix "--input-vcf" ] ; sld:type cwl:File , xsd:string . cwl:source . rdfs:comment "Two-column sample file listing sample name and tumor or control" ; cwl:inputBinding [ CommandLineBinding:prefix "--samples" ] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . rdfs:comment "Sorted tumor bam" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Variant calling center to report in MAF" ; cwl:default "mskcc.org" ; cwl:inputBinding [ CommandLineBinding:prefix "--maf-center" ] ; sld:type xsd:string , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:valueFrom "${ return inputs.sed_file.basename.replace(\".columns_added.txt\", \".portal.txt\"); }" . rdfs:comment "include regions marked in this genome" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--all_regions" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; sld:type cwl:File . cwl:valueFrom "${ return \"tn_pair.txt\"; }" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type cwl:File . sld:type cwl:File . cwl:valueFrom "${ return inputs.grepped_file.basename.replace(\".grepped.txt\", \".extracted.txt\"); }" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "genome fasta file" ; cwl:inputBinding [ CommandLineBinding:prefix "--genome" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:source . sld:type xsd:string . sld:type cwl:File . cwl:source . rdfs:comment " Output duplicate records present in multiple files only once - " ; cwl:inputBinding [ CommandLineBinding:prefix "--rm-dups" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--rm-dups" ] ; sld:type xsd:string , sld:null . cwl:valueFrom "${ return inputs.tumor_sample_name + \"\\ttumor\\n\" + inputs.normal_sample_name + \"\\tcontrol\"; }" . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . a cwl:CommandLineTool ; cwl:baseCommand ( "sed" "1s/$/\\tDNA_support\\tRNA_support/;2,$s/$/\\tyes\\tno/" ) ; cwl:baseCommand ( "sed" "1s/$/\\tDNA_support\\tRNA_support/;2,$s/$/\\tyes\\tno/" ) ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "alpine:3.8" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "alpine:3.8" ] ; cwl:stdout "$(inputs.output_filename)" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "Matched normal ID used in VCFs genotype columns" ; cwl:default "NORMAL" ; cwl:inputBinding [ CommandLineBinding:prefix "--vcf-normal-id" ] ; sld:type xsd:string , sld:null . rdfs:comment "log stdout to file" ; cwl:inputBinding [ CommandLineBinding:prefix "--stdout" ] ; sld:type xsd:string , sld:null . rdfs:comment "max. fractional ALT support in control" ; cwl:default 0 ; cwl:inputBinding [ CommandLineBinding:prefix "--controlcontamination" ] ; sld:type xsd:int , sld:null . cwl:source . rdfs:comment "max. SV size" ; cwl:default 500000000 ; cwl:inputBinding [ CommandLineBinding:prefix "--maxsize" ] ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; sld:type cwl:File . cwl:source . rdfs:comment "file with regions to exclude" ; cwl:inputBinding [ CommandLineBinding:prefix "--exclude" ] ; sld:type cwl:File , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "do not append version and command line to the header" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--no-version" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--no-version" ] ; sld:type xsd:boolean , sld:null . rdfs:comment "Number of variants VEP loads at a time; Reduce this for low memory systems" ; cwl:default 5000 ; cwl:inputBinding [ CommandLineBinding:prefix "--buffer-size" ] ; sld:type xsd:int , sld:null . cwl:valueFrom "${ return true; }" . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Use tag common_variant if the filter-vcf reports a subpopulation AC higher than this" ; cwl:default 10 ; cwl:inputBinding [ CommandLineBinding:prefix "--max-filter-ac" ] ; sld:type xsd:int , sld:null . rdfs:comment "Input file (.bcf)" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "log stderr to file" ; cwl:inputBinding [ CommandLineBinding:prefix "--stderr" ] ; sld:type xsd:string , sld:null . rdfs:comment "SV type (DEL, DUP, INV, BND, INS)" ; cwl:default "DEL" ; cwl:inputBinding [ CommandLineBinding:prefix "--type" ] ; sld:type xsd:string , sld:null . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:in , , , , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Version of VEP and its cache to use" ; cwl:default "86" ; cwl:inputBinding [ CommandLineBinding:prefix "--cache-version" ] ; sld:type xsd:string , sld:null . cwl:valueFrom "${ return true; }" . a cwl: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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . a cwl:CommandLineTool ; cwl:baseCommand ( "grep" "^[^#;]" ) ; cwl:baseCommand ( "grep" "^[^#;]" ) ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "alpine:3.8" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "alpine:3.8" ] ; cwl:stdout "$(inputs.output_filename)" . cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.o)\n return inputs.o;\n return null;\n}\n" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "insert size cutoff, median+s*MAD (deletions only)" ; cwl:default 9 ; cwl:inputBinding [ CommandLineBinding:prefix "--mad-cutoff" ] ; sld:type xsd:int , sld:null . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . a cwl:CommandLineTool ; rdfs:comment "None\n" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/delly" "call" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.x)" , "$(inputs.normal_bam)" , "$(inputs.tumor_bam)" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mskcc/roslin-variant-delly:0.7.7" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . a cwl:CommandLineTool ; rdfs:label "cmo-index" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "cmo_index" ) ; cwl:baseCommand ( "cmo_index" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mskcc/roslin-variant-cmo-utils:1.9.15" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.bam)" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mskcc/roslin-variant-cmo-utils:1.9.15" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.bam)" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 16000 ] . rdfs:comment " Write output to a file [standard output]" ; cwl:default "bcftools_concat.vcf" ; cwl:inputBinding [ CommandLineBinding:prefix "--output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--output" ] ; sld:type xsd:string . sld:type xsd:string . cwl:source . cwl:valueFrom "${ return inputs.input_maf.basename.replace(\".maf\", \".grepped.txt\"); }" . cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output_maf)\n return inputs.output_maf;\n return null;\n}\n" ] ; sld:type cwl:File . rdfs:comment "Filtered SV BCF output file" ; cwl:default "sv.bcf" ; cwl:inputBinding [ CommandLineBinding:prefix "--outfile" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:comment "None\n" ; rdfs:label "vcf2maf" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:prefix "--tmp-dir" ; CommandLineBinding:shellQuote false ; cwl:valueFrom "$(runtime.tmpdir)" ] ) ; cwl:baseCommand ( "perl" "/usr/bin/vcf2maf/vcf2maf.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 "mskcc/roslin-variant-vcf2maf:1.6.17" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 2 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "log stdout to file" ; cwl:inputBinding [ CommandLineBinding:prefix "--stdout" ] ; sld:type xsd:string , sld:null . sld:type xsd:string . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . rdfs:comment "If GT undefined in VCF, minimum allele fraction to call a variant homozygous" ; cwl:default 7e-01 ; cwl:inputBinding [ CommandLineBinding:prefix "--min-hom-vaf" ] ; sld:type xsd:float , sld:null . rdfs:comment "Tumor_Sample_Barcode to report in the MAF" ; cwl:default "TUMOR" ; cwl:inputBinding [ CommandLineBinding:prefix "--tumor-id" ] ; sld:type xsd:string , sld:null . rdfs:comment "no small InDel calling" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--noindels" ] ; sld:type xsd:boolean , sld:null . a cwl:Workflow ; Workflow:steps , ; cwl:inputs , , , , , , , , ; cwl:outputs , . cwl:source . cwl:valueFrom "${ return inputs.i.basename.replace(\".bcf\", \".pass.bcf\"); }" . sld:type xsd:string . rdfs:comment "Comma-delimited names of INFO fields to retain as extra columns in MAF" ; cwl:inputBinding [ CommandLineBinding:prefix "--retain-info" ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*.pass.bcf" ] ; cwl:outputSource ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:source . sld:type xsd:string . sld:type xsd:string . a cwl:CommandLineTool ; cwl:baseCommand ( "echo" "-e" ) ; cwl:baseCommand ( "echo" "-e" ) ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "alpine:3.8" ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "alpine:3.8" ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:stdout "$(inputs.output_filename)" . cwl:source . rdfs:comment "Array of vcf files to be concatenated into one vcf" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "min. read-depth ratio of carrier vs. non-carrier for a duplication" ; cwl:default 1.2e+00 ; cwl:inputBinding [ CommandLineBinding:prefix "--rddup" ] ; sld:type xsd:float , sld:null . rdfs:comment "Ligate phased VCFs by matching phase at overlapping haplotypes" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--ligate" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--ligate" ] ; sld:type xsd:boolean , sld:null . cwl:source . rdfs:comment "Genome build of variants in input" ; cwl:default "GRCh37" ; cwl:inputBinding [ CommandLineBinding:prefix "--ncbi-build" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type xsd:string . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . rdfs:comment "Path to output MAF file" ; cwl:inputBinding [ CommandLineBinding:prefix "--output-maf" ] ; sld:type xsd:string , sld:null . rdfs:comment "SV type (DEL, DUP, INV, BND, INS)" ; cwl:default "DEL" ; cwl:inputBinding [ CommandLineBinding:prefix "--type" ] ; sld:type xsd:string , sld:null . rdfs:comment "Concatenate BCF files without recompression (dangerous, use with caution)" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--naive" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--naive" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:comment "None\n" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/delly" "filter" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mskcc/roslin-variant-delly:0.7.7" ] . cwl:source . rdfs:comment "max. read-depth ratio of carrier vs. non-carrier for a deletion" ; cwl:default 8e-01 ; cwl:inputBinding [ CommandLineBinding:prefix "--rddel" ] ; sld:type xsd:float , sld:null . cwl:valueFrom "$(inputs.input_vcf.basename.replace('vcf','vep.maf'))" . rdfs:comment "Reference FASTA file" ; cwl:inputBinding [ CommandLineBinding:prefix "--ref-fasta" ] ; sld:type cwl:File , sld:null . rdfs:comment "Filter sites for PASS" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:prefix "--pass" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output)\n return inputs.output;\n return null;\n}" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output)\n return inputs.output;\n return null;\n}" ] ; sld:type cwl:File . cwl:valueFrom "${ return inputs.tumor_sample_name + \".\" + inputs.normal_sample_name + \".svs.pass.vcf\"; }" . rdfs:comment " Restrict to regions listed in a file" ; cwl:inputBinding [ CommandLineBinding:prefix "--regions-file" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--regions-file" ] ; sld:type xsd:string , sld:null . rdfs:comment "Tumor sample ID used in VCFs genotype columns" ; cwl:default "TUMOR" ; cwl:inputBinding [ CommandLineBinding:prefix "--vcf-tumor-id" ] ; sld:type xsd:string , sld:null . rdfs:comment "Sorted normal bam" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "SV BCF output file" ; cwl:default "sv.bcf" ; cwl:inputBinding [ CommandLineBinding:prefix "--outfile" ] ; sld:type xsd:string , sld:null . rdfs:comment "List of custom ENST IDs that override canonical selection" ; cwl:inputBinding [ CommandLineBinding:prefix "--custom-enst" ] ; sld:type xsd:string , sld:null . cwl:in , ; cwl:out ; cwl:run .