@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 . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:string . a cwl:CommandLineTool ; rdfs:comment "Fillout allele counts for a MAF file using GetBaseCountsMultiSample on BAMs\n" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--n_threads" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:arguments ( [ CommandLineBinding:position 0 ; CommandLineBinding:prefix "--n_threads" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "cmo_fillout" ) ; cwl:baseCommand ( "cmo_fillout" ) ; 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:coresMin 6 ; ResourceRequirement:ramMin 48000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mskcc/roslin-variant-cmo-utils:1.9.15" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mskcc/roslin-variant-cmo-utils:1.9.15" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 6 ; ResourceRequirement:ramMin 48000 ] . sld:type xsd:string . rdfs:comment "Input maf file which needs to be tagged" ; cwl:inputBinding [ CommandLineBinding:prefix "--input-maf" ] ; sld:type cwl:File . sld:type xsd:string . rdfs:comment "Reference assembly file of BAM files, e.g. hg19/grch37/b37" ; cwl:inputBinding [ CommandLineBinding:prefix "--ref-fasta" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--ref-fasta" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type [ sld:items xsd:string ; 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:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type [ sld:fields , , , , , , , , , , , , , ; sld:type sld:record ] . sld:type xsd:string . cwl:source . rdfs:comment "make lots of noise" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--verbose" ] ; sld:type xsd:boolean , sld:null . sld:type xsd:string . cwl:valueFrom "${ return inputs.tumor_sample_name + \".\" + inputs.normal_sample_name + \".muts.maf\" }" . rdfs:comment "BAM files to fillout with" ; cwl:inputBinding [ CommandLineBinding:prefix "--bams" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--bams" ] ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] ; sld:type [ sld:items cwl:File , xsd:string ; sld:type sld:array ] . sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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:in , , , , , , , , , , , , , ; cwl:out ; cwl:run . 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 . rdfs:comment "Output maf file name" ; cwl:inputBinding [ CommandLineBinding:prefix "--output-maf" ] ; sld:type xsd:string . cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . a cwl:CommandLineTool ; rdfs:comment "This tool flags false-positive somatic calls in a given MAF file\n" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "python" "/usr/bin/ngs-filters/run_ngs-filters.py" ) ; 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:DockerRequirement ; DockerRequirement:dockerPull "mskcc/roslin-variant-ngs-filters:1.4" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 3 ; ResourceRequirement:ramMin 36000 ] . 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:source . cwl:source . rdfs:comment "Path to input file in VCF format" ; cwl:inputBinding [ CommandLineBinding:prefix "--input-vcf" ] ; sld:type cwl:File , xsd:string . rdfs:comment "Folder containing variant_effect_predictor.pl or vep binary" ; cwl:inputBinding [ CommandLineBinding:prefix "--vep-path" ] ; sld:type xsd:string , sld:null . rdfs:comment "Input txt file which has hotspots" ; cwl:inputBinding [ CommandLineBinding:prefix "--input-hotspot" ] ; sld:type cwl:File , xsd:string , sld:null . sld:type xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . rdfs:comment "Path to fillout maf file of panel of standard normals" ; cwl:inputBinding [ CommandLineBinding:prefix "--normal-panel-maf" ] ; sld:type cwl:File , xsd:string , sld:null . cwl:default "1" . sld:type [ sld:items xsd:string ; sld:type sld:array ] . 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mskcc/roslin-variant-vcf2maf:1.6.17" ] . rdfs:comment "make lots of noise" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:prefix "--verbose" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:comment "Remove snps/indels from the output maf where a complex variant is called\n" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "python" "/usr/bin/remove_variants.py" ) ; 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 3 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mskcc/roslin-variant-remove-variants:0.1.1" ] . sld:type [ sld:items xsd:string ; sld:type sld:array ] . 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 . cwl:in , , ; cwl:out ; cwl:run . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:valueFrom "${ return inputs.maf.basename.replace(\".maf\", \".curated.fillout\"); }" . rdfs:comment "Tab separated pairing file, normal tumor" ; cwl:inputBinding [ CommandLineBinding:prefix "--pairing-file" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--pairing-file" ] ; sld:type cwl:File , 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 "Precomputed fillout file from GBCMS (using this skips GBCMS)" ; cwl:inputBinding [ CommandLineBinding:prefix "--fillout" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--fillout" ] ; sld:type xsd:string , sld:null . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . 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 . cwl:source . cwl:source . rdfs:comment "Reference FASTA file" ; cwl:inputBinding [ CommandLineBinding:prefix "--ref-fasta" ] ; sld:type cwl:File , sld:null . cwl:source . sld:type xsd:string . cwl:source . sld:type xsd:string . rdfs:comment "File with list of normal samples" ; cwl:inputBinding [ CommandLineBinding:prefix "--normalSamplesFile" ] ; sld:type xsd:string , sld:null . sld:type [ sld:fields ; sld:type sld:record ] ; sld:type [ sld:fields ; sld:type sld:record ] . cwl:default "1" . sld:type xsd:string . sld:type xsd:string . 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 . rdfs:comment "Filename for output of raw fillout data in MAF/VCF format" ; cwl:inputBinding [ CommandLineBinding:prefix "--output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--output" ] ; 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 . sld:type xsd:string . cwl:source . 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:secondaryFiles [] ; sld:type cwl:File . cwl:source . 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 . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type [ sld:fields ; sld:type sld:record ] ; sld:type [ sld:fields ; sld:type sld:record ] . cwl:in , , , , ; cwl:out ; cwl:run . cwl:valueFrom "${ return inputs.inputMaf.basename.replace(\".vep.maf\", \".vep.rmv.maf\") }" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Genome build of variants in input" ; cwl:default "GRCh37" ; cwl:inputBinding [ CommandLineBinding:prefix "--ncbi-build" ] ; sld:type xsd:string , sld:null . sld:type xsd:string . 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 . 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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.outputMaf)\n return inputs.outputMaf;\n return null;\n}\n" ] ; sld:type cwl:File . sld:type xsd:string . rdfs:comment "Output format MAF(1) or tab-delimited with VCF based coordinates(2)" ; cwl:inputBinding [ CommandLineBinding:prefix "--format" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--format" ] ; sld:type xsd:string . sld:type xsd:string . rdfs:comment "List of custom ENST IDs that override canonical selection" ; cwl:inputBinding [ CommandLineBinding:prefix "--custom-enst" ] ; sld:type xsd:string , sld:null . rdfs:comment "Species of variants in input" ; cwl:default "homo_sapiens" ; cwl:inputBinding [ CommandLineBinding:prefix "--species" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; cwl:baseCommand ( "echo" "-e" ) ; cwl:baseCommand ( "echo" "-e" ) ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "alpine:3.8" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "alpine:3.8" ] ; cwl:stdout "$(inputs.output_filename)" . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Output maf file name" ; cwl:inputBinding [ CommandLineBinding:prefix "--output-maf" ] ; sld:type xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string . cwl:default "QUAL,BIAS,HIAF,PMEAN,PSTD,ALD,RD,NM,MQ,IS" . cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.portal_output)\n return inputs.portal_output;\n else\n return inputs.maf.basename.replace(\".maf\", \".fillout.portal.maf\");\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.portal_output)\n return inputs.portal_output;\n else\n return inputs.maf.basename.replace(\".maf\", \".fillout.portal.maf\");\n}\n" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; sld:type cwl:File . rdfs:comment "Path to fillout maf file of cohort normals" ; cwl:inputBinding [ CommandLineBinding:prefix "--normal-cohort-maf" ] ; sld:type cwl:File , xsd:string , sld:null . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output_maf)\n return inputs.output_maf;\n return null;\n}\n" ] ; sld:type cwl:File . rdfs:comment "VEPs base cache/plugin directory" ; cwl:inputBinding [ CommandLineBinding:prefix "--vep-data" ] ; sld:type xsd:string , sld:null . cwl:valueFrom "${ return \"tn_pairing_file.txt\"; }" . cwl:source . cwl:source . cwl:valueFrom "${ return inputs.tumor_id + \".\" + inputs.normal_id + \".combined-variants.vep.maf\" }" . cwl:in , ; cwl:out ; cwl:run . rdfs:comment "Input maf file which needs to be fixed" ; cwl:inputBinding [ CommandLineBinding:prefix "--input-maf" ] ; sld:type cwl:File , xsd:string . rdfs:comment "MAF file on which to fillout" ; cwl:inputBinding [ CommandLineBinding:prefix "--maf" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--maf" ] ; sld:type cwl:File . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:default "set,TYPE,FAILURE_REASON,MSI,MSILEN,SSF,LSEQ,RSEQ,STATUS,VSB" . sld:type xsd:string . rdfs:comment "The non-TCGA VCF from exac.broadinstitute.org" ; cwl:inputBinding [ CommandLineBinding:prefix "--filter-vcf" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . cwl:source . sld:type [ sld:fields , , , , , , , , , , , , , ; sld:type sld:record ] . cwl:source . rdfs:comment "Use tag common_variant if the filter-vcf reports a subpopulation AC higher than this" ; cwl:default 10 ; cwl:inputBinding [ CommandLineBinding:prefix "--max-filter-ac" ] ; sld:type xsd:int , sld:null . sld:type xsd:string . rdfs:comment "Filename for a portal-friendly output MAF" ; cwl:inputBinding [ CommandLineBinding:prefix "--portal-output" ] ; cwl:inputBinding [ CommandLineBinding:prefix "--portal-output" ] ; sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output)\n return inputs.output;\n else\n return inputs.maf.basename.replace(\".maf\", \".fillout\");\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.output)\n return inputs.output;\n else\n return inputs.maf.basename.replace(\".maf\", \".fillout\");\n}\n" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "${\n if (inputs.outputMaf )\n return inputs.outputMaf;\n return null;\n}\n" ] ; sld:type cwl:File . sld:type xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:valueFrom "${ return inputs.normal.ID + \"\\t\" + inputs.tumor.ID; }" . a cwl:Workflow ; Workflow:steps ; cwl:inputs , , ; cwl:outputs . cwl:in , , , ; cwl:out ; cwl:run . 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 . sld:type xsd:string . sld:type xsd:string . cwl:source . sld:type xsd:string . rdfs:comment "When reporting co-located variants, allow mismatched variant alleles too" ; cwl:inputBinding [ CommandLineBinding:prefix "--any-allele" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:source . sld:type cwl:File . cwl:source . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Full Path to the output dir." ; cwl:inputBinding [ CommandLineBinding:prefix "--outDir" ] ; sld:type xsd:string , sld:null . rdfs:comment "Path to output MAF file" ; cwl:inputBinding [ CommandLineBinding:prefix "--output-maf" ] ; sld:type xsd:string , sld:null .