@prefix LoadListingRequirement: . @prefix SchemaDefRequirement: . @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: . @prefix ExpressionTool: . cwl:outputSource ; 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:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:in , , , , , , , , ; cwl:out , , , , ; cwl:run . sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File , sld:null . sld:type xsd:string . a cwl:Workflow ; rdfs:label "scatter GATK HaplotypeCaller over intervals" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename).flagstat" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "GATK HaplotypeCaller" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "HaplotypeCaller" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.5.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 10000 ] . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "--vcf" ] ; sld:type cwl:File . cwl:source . cwl:default "cnvkit" . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "source caller of the vcf input file" ; cwl:inputBinding [ CommandLineBinding:position 6 ] ; cwl:inputBinding [ CommandLineBinding:position 6 ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).NameSorted.bam" ] ; sld:type cwl:File . cwl:source . rdfs:comment "if true, outputs assembled contig sequences in final VCF files, in the INFO field CONTIG" ; cwl:inputBinding [ CommandLineBinding:position -7 ; CommandLineBinding:prefix "--outputContig" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:default "v" . cwl:source . cwl:source . cwl:default "variants" ; sld:type xsd:string , sld:null . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File , sld:null . cwl:default "smoove" . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--cnr" ] ; sld:type cwl:File , sld:null . rdfs:comment "method for filtering/merging neighboring copy number segments" ; cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--filter" ] ; sld:type sld:null ; sld:type [ sld:symbols , , , ; sld:type sld:enum ] . cwl:source . cwl:default "bcftools-merged-AnnotSV.tsv" . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--threads" "$(runtime.cores)" ) ; cwl:arguments ( "--threads" "$(runtime.cores)" ) ; cwl:baseCommand ( "/usr/bin/duphold" ) ; cwl:baseCommand ( "/usr/bin/duphold" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/duphold-cwl:0.1.5" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 10000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 10000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/duphold-cwl:0.1.5" ] . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:in , ; cwl:out , ; cwl:run . cwl:source . cwl:source . rdfs:comment "Minimum number of sv calls needed to be merged" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:int . cwl:in ; cwl:out ; cwl:run . rdfs:comment "Depth for duplications must be greater than this cutoff to pass the filter." ; cwl:default 1.25e+00 ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:double , sld:null . sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).GcBiasMetricsSummary.txt" ] ; sld:type cwl:File . cwl:source . rdfs:comment "method for size filtering" ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . cwl:in , , , , ; cwl:out ; cwl:run . rdfs:comment "vcf file to filter" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cram.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('fastq2')? self.sequence.fastq2 : null)" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:default true . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-BQSR" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type cwl:File , sld:null . cwl:source . rdfs:comment "List of chromosomes to run CNVnator on" ; cwl:default "chr9" , "chr11" , "chr22" , "chr18" , "chrX" , "chr5" , "chr15" , "chr13" , "chr21" , "chr8" , "chr2" , "chr6" , "chr17" , "chr4" , "chr10" , "chr1" , "chr20" , "chr12" , "chrY" , "chr7" , "chr16" , "chr14" , "chr3" , "chr19" ; cwl:inputBinding [ CommandLineBinding:itemSeparator " " ; CommandLineBinding:position 3 ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:type xsd:int . cwl:source . rdfs:comment "Reference used to generate the bams" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "INTERVALS=" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "AnnotSV" "-bedtools" "/usr/bin/bedtools" "-outputDir" "$(runtime.outdir)" ) ; cwl:arguments ( "AnnotSV" "-bedtools" "/usr/bin/bedtools" "-outputDir" "$(runtime.outdir)" ) ; 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:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/annotsv-cwl:2.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/annotsv-cwl:2.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] . cwl:source . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "output vcf file name" ; cwl:default "filtered_cnv.vcf" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string , sld:null . a cwl:Workflow ; rdfs:label "Subworkflow to allow calling different SV callers which require bam files as inputs" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--diagram" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; sld:type cwl:File . rdfs:comment "number of alternate paired reads support needed to pass" ; cwl:default 2 ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:int , sld:null . rdfs:comment "bgzip-compressed, tabix-indexed BED file specifiying regions to which variant analysis will be restricted" ; cwl:inputBinding [ CommandLineBinding:position -5 ; CommandLineBinding:prefix "--callRegions" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . sld:type cwl:File , sld:null . cwl:source . sld:type xsd:int , sld:null . cwl:source . cwl:default "chr17" , "chr20" , "chr12" , "chr21" , "chr15" , "chr13" , "chr1" , "chr8" , "chr10" , "chr4" , "chr11" , "chr9" , "chr6" , "chr5" , "chr22" , "chr2" , "chr18" , "chr7" , "chr19" , "chr3" , "chr16" , "chr14" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "wgs alignment and germline variant detection" ; 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:SchemaDefRequirement ; SchemaDefRequirement:types , ] . sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:default false . sld:type xsd:double , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "samtools flagstat" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "flagstat" ) ; 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/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.bam.basename).flagstat" . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "Samtools: merge" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(inputs.name).merged.bam" [ CommandLineBinding:prefix "--threads" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "merge" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] . sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "sort BAM by name" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-t" [ cwl:valueFrom "$(runtime.cores)" ] "-m" "22G" "-n" "-o" [ cwl:valueFrom "$(inputs.bam.nameroot).NameSorted.bam" ] ) ; cwl:baseCommand ( "/usr/bin/sambamba" "sort" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/sambamba-cwl:0.6.4" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 24000 ] . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type xsd:double , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "${\n var glob_base = \".antitargetcoverage.cnn\";\n if (inputs.normal_bam) {\n glob_base = inputs.normal_bam.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position -2 ; CommandLineBinding:prefix "--normalBam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "${\n var glob_base = \".target.bed\";\n if (inputs.bait_intervals) {\n glob_base = inputs.bait_intervals.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ; sld:type cwl:File , sld:null . rdfs:comment "Estimate distance based on the size of SV" ; cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\n if(inputs.estimate_sv_distance){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n" ] ; sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; sld:type xsd:boolean , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "bcftools-sv-merged.vcf" . cwl:in ; cwl:out , ; cwl:run . cwl:source . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . sld:type xsd:string . a cwl:Workflow ; rdfs:label "HS Metrics workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , ; cwl:outputs , , , , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "collect WGS metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).WgsMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectWgsMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:default "min_len" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-ERC" ] ; sld:type xsd:string . cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "output vcf file name" ; cwl:default "bcftools_merged.vcf.gz" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--output" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "verify BAM ID" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--out" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).VerifyBamId" ] ) ; cwl:baseCommand ( "/usr/local/bin/verifyBamID" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/verify_bam_id-cwl:1.1.3" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GQB" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(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 "$(self.basename)" ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "Run SURVIVOR to merge SV calls" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/bin/bash" "/usr/bin/survivor_merge_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/survivor-cwl:1.0.6.2" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 2000 ] . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Convert default cnvkit .cns output to standard vcf format" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position -1 ; CommandLineBinding:prefix "-y" ; cwl:valueFrom "$(inputs.male_reference)" ] "-o" "adjusted.tumor.cns" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "&&" ] "/usr/bin/python" "/usr/local/bin/cnvkit.py" "export" "vcf" "adjusted.tumor.cns" ) ; cwl:baseCommand ( "/usr/bin/python" "/usr/local/bin/cnvkit.py" "call" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "etal/cnvkit:0.9.5" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:default "flag_pick" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--" ; CommandLineBinding:separate false ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . sld:type xsd:int , sld:null . cwl:source . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:in , , , , ; cwl:out , , , , ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_size.sh" ) ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_size.sh" ) ; 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:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nINPUT_VCF=\"$1\"\nOUTPUT_VCF=\"$2\"\nSV_SIZE=\"$3\"\nFILTER_METHOD=\"$4\"\n\nif [ \"$FILTER_METHOD\" == \"max_len\" ]; then\n echo \"Running filter for max size svs\"\n filter_expression=\"ABS(SVLEN) <= $SV_SIZE\"\nelif [ \"$FILTER_METHOD\" == \"min_len\" ]; then\n echo \"Running filter for min size svs\"\n filter_expression=\"ABS(SVLEN) >= $SV_SIZE\"\nelse\n echo \"Filter method: '$FILTER_METHOD' is not supported for size SV filtering\"\n exit 1\nfi\n/opt/bcftools/bin/bcftools filter \"$INPUT_VCF\" -o \"$OUTPUT_VCF\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_size.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nINPUT_VCF=\"$1\"\nOUTPUT_VCF=\"$2\"\nSV_SIZE=\"$3\"\nFILTER_METHOD=\"$4\"\n\nif [ \"$FILTER_METHOD\" == \"max_len\" ]; then\n echo \"Running filter for max size svs\"\n filter_expression=\"ABS(SVLEN) <= $SV_SIZE\"\nelif [ \"$FILTER_METHOD\" == \"min_len\" ]; then\n echo \"Running filter for min size svs\"\n filter_expression=\"ABS(SVLEN) >= $SV_SIZE\"\nelse\n echo \"Filter method: '$FILTER_METHOD' is not supported for size SV filtering\"\n exit 1\nfi\n/opt/bcftools/bin/bcftools filter \"$INPUT_VCF\" -o \"$OUTPUT_VCF\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_size.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--targets" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . rdfs:comment "output vcf file name" ; cwl:default "filtered_sv_size.vcf" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string , sld:null . sld:type , . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . sld:type xsd:string . cwl:source . cwl:default false . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--dir" ] ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "collect alignment summary metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "OUTPUT=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . cwl:in , , , , , , , , ; cwl:out , , , , , , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--normal" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type cwl:File . rdfs:comment "Array of bams to run through lumpy, can be single or small cohort" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--genotype" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:boolean , sld:null . cwl:default "none" . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--input" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "${ return [ self ]; }" . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-y" ] ; sld:type xsd:boolean , sld:null . cwl:source . a cwl:Workflow ; rdfs:label "Merge, annotate, and generate a TSV for SVs" ; 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.depthSM" ] ; sld:type cwl:File . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; sld:type xsd:int , sld:null . cwl:in , , , ; cwl:out ; cwl:run . cwl:in , , , , , , ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Require merged SVs to be on the same strand" ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "${\n if(inputs.same_strand){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n" ] ; sld:type xsd:boolean . sld:type xsd:int , sld:null . cwl:in , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/tumorSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:default "cn" . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "collect insert size metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] "H=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ; 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 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] . cwl:default "final" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('fastq1')? self.sequence.fastq1 : null)" . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:default "cnvnator" . cwl:outputBinding [ CommandOutputBinding:glob "bqsr.table" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . a cwl:Workflow ; rdfs:label "Subworkflow that runs cnvkit in single sample mode and returns a vcf file" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , ; cwl:outputs , , , , , , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "samtools index" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.bam.basename)" "$(runtime.outdir)/$(inputs.bam.basename).bai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.bam.basename).bai" "$(runtime.outdir)/$(inputs.bam.nameroot).bai" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.bam; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:in , , , , , , , , , , ; cwl:out ; cwl:run . cwl:source . sld:type xsd:string . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).cns" ] ; sld:type cwl:File . cwl:source . sld:type xsd:int . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).targetcoverage.cnn" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default "Wildtype" , "Downstream" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default false . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type xsd:string . sld:type xsd:int . cwl:source . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--drop-low-coverage" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "Run CNVnator to calculate copy number variations in WGS samples" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "source" "/opt/root/bin/thisroot.sh" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "&&" ] "/bin/bash" "run_cnvnator.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/cnvnator-cwl:0.4" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\n# set vars\nBAM=\"$1\"\nBIN_SIZE=\"$2\"\nCHROMOSOMES=\"$3\"\nREFERENCE=\"$4\"\nSAMPLE=\"$5\"\n\n# create directory to store fasta files. CNVnator wants chromosomes in individual files\n# while with later versions of CNVnator these steps will accept a fasta.gz file the cnvnator2VCF.pl will not\nmkdir FASTA_CHRS\nawk 'BEGIN { CHROM=\"\" } { if ($1~\"^>\") CHROM=substr($1,2); print $0 > \"FASTA_CHRS/\"CHROM\".fa\" }' \"$REFERENCE\"\n \n# extract read mapping from input bam(single sample)\ncnvnator -root \"${SAMPLE}.root\" -tree \"$BAM\" -chrom $CHROMOSOMES\n# generate read depth histogram\ncnvnator -root \"${SAMPLE}.root\" -his \"${BIN_SIZE}\" -d FASTA_CHRS/ -chrom $CHROMOSOMES\n# calculate statistics\ncnvnator -root \"${SAMPLE}.root\" -stat \"${BIN_SIZE}\" -chrom $CHROMOSOMES\n# read depth signal partitioning\ncnvnator -root \"${SAMPLE}.root\" -partition \"${BIN_SIZE}\" -chrom $CHROMOSOMES\n# cnv calling\ncnvnator -root \"${SAMPLE}.root\" -call \"${BIN_SIZE}\" -chrom $CHROMOSOMES > \"${SAMPLE}.CNVnator.cn\"\n\n# convert to vcf\ncnvnator2VCF.pl -reference \"$REFERENCE\" \"${SAMPLE}.CNVnator.cn\" FASTA_CHRS/ > \"${SAMPLE}.CNVnator.vcf\"\nexit 0\n" ; cwl:entryname "run_cnvnator.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 20000 ; ResourceRequirement:tmpdirMin 10000 ] . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:in , , , , , , , , , , ; cwl:out , ; cwl:run . sld:type cwl:File . cwl:default "MarkedSorted.bam" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string , sld:null . sld:type xsd:boolean , sld:null . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-contamination" ] ; sld:type xsd:string , sld:null . rdfs:comment "Reference used to generate the alignments" ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:source . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "target-$(self.label)" . sld:type xsd:string . sld:type xsd:boolean , sld:null . cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . 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 [] ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).GcBiasMetricsChart.pdf" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-y" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . rdfs:comment "Bed file used to exclude regions" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:default "ALL_READS" ; sld:type xsd:string , sld:null . cwl:source . sld:type xsd:int , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:double , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "refAlign.bam" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:default "hybrid" ; sld:type xsd:string , sld:null . cwl:source . sld:fields ; sld:type sld:record . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . sld:type xsd:string , sld:null . cwl:default "final" ; sld:type xsd:string , sld:null . sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cohort_name)-smoove.genotyped.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; sld:type xsd:boolean , sld:null . cwl:source ; cwl:valueFrom "${ return [ self ]; }" . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; sld:type cwl:File , sld:null . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--synonyms" ] ; sld:type cwl:File , sld:null . cwl:source ; cwl:valueFrom "base-$(self.label)" . cwl:default "queryname" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , ; cwl:out ; cwl:run . sld:type xsd:boolean , sld:null . cwl:source . cwl:source . sld:type xsd:int . cwl:valueFrom "ALL_READS" . cwl:outputBinding [ CommandOutputBinding:glob "genotype.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "BAM to CRAM conversion" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "view" "-C" ) ; 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/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.bam.nameroot).cram" . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . a cwl:Workflow ; rdfs:label "Raw sequence data to BQSR" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:double , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . rdfs:comment "Maximum distance of variants to consider for merging" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:int . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "${\n var glob_base = \".targetcoverage.cnn\";\n if (inputs.normal_bam) {\n glob_base = inputs.normal_bam.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot)-diagram.pdf" ] ; sld:type cwl:File , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:boolean . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:int , sld:null . cwl:source . sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_tsv_name)" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:in , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-T" ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:string . sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:default "filtered_cnvkit.vcf" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somaticSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string , sld:null . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('bam')? self.sequence.bam : null)" . sld:type xsd:int . cwl:outputSource ; sld:type cwl:File . sld:type xsd:double , sld:null . sld:type xsd:double , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name).bam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/candidateSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "WGS QC workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs , , , , , , , , , , , , , , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "reference.cnn" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "output file format" ; cwl:default "z" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--output-type" ] ; sld:type [ sld:symbols , , , ; sld:type sld:enum ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--everything" ] ; sld:type xsd:boolean , sld:null . cwl:source ; cwl:valueFrom "summary-$(self.label)" . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . rdfs:comment "toggles on settings for WES" ; cwl:inputBinding [ CommandLineBinding:position -6 ; CommandLineBinding:prefix "--exome" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:default "SURVIVOR-sv-merged.vcf" . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--allowMissingData" "-o" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantsToTable" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . rdfs:comment "vcf file to filter" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-SVinputFile" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-SVinputFile" ] ; sld:type cwl:File . cwl:in , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).antitargetcoverage.cnn" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:default "ID" , "ALT" , "CHROM" , "POS" , "REF" , "set" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . sld:type [ sld:items ; sld:type sld:array ] . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-b" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "${ \n var glob_base = \".antitarget.bed\";\n if (inputs.bait_intervals) {\n glob_base = inputs.bait_intervals.nameroot + glob_base;\n } \n return glob_base;\n} \n" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-2" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:default "cnvnator" . cwl:source . sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--scatter" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_tsv_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_tsv_name)" ] ; sld:type cwl:File . cwl:default "SURVIVOR-merged-AnnotSV.tsv" . cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "GATK HaplotypeCaller" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" "genotype.vcf.gz" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "GenotypeGVCFs" ) ; 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:3.5.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:source . sld:type xsd:boolean . cwl:in , , ; cwl:out , , ; cwl:run . cwl:source . cwl:source . sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.selfSM" ] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ; sld:type cwl:File . rdfs:comment "source caller of the vcf input file" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--dbsnp" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:default "variants" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . rdfs:comment "snps vcf file to annotate hom/het variant counts within sv" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--snp" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--snp" ] ; sld:type cwl:File , sld:null . a cwl:Workflow ; rdfs:label "exome alignment and germline variant detection" ; 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 ] . rdfs:comment "include genotypes from this sample" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . rdfs:comment "size in bp used for filtering" ; cwl:default 50000 ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:int , sld:null . cwl:default "output.g.vcf.gz" ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type xsd:int , sld:null . cwl:source . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 9 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--plugin" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:default "filtered-bcftools-merged-AnnotSV.tsv" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--output" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type xsd:string , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "collect gc bias metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).GcBiasMetrics.txt" ] "CHART=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).GcBiasMetricsChart.pdf" ] "S=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).GcBiasMetricsSummary.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectGcBiasMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . sld:type xsd:boolean . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . rdfs:comment "vcf file to filter" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cohort_name)" ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "Filter single sample sv vcf from paired read callers(Manta/Smoove)" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:source . sld:type xsd:int . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:default "manta" . cwl:source . cwl:source . sld:type xsd:string , sld:null . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(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 "$(inputs.file.basename).gz" ] ; sld:type cwl:File . cwl:default "filtered_manta.vcf" . cwl:default "0.05" . cwl:outputBinding [ CommandOutputBinding:glob "annotated.vcf_summary.html" ] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "apply BQSR" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_name).bam" ] "-preserveQ" "6" "-SQQ" "10" "-SQQ" "20" "-SQQ" "30" "-nct" "8" "--disable_indel_quals" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "PrintReads" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "sv vcf file to annotate" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--vcf" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--vcf" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default "AD" , "AF" , "DP" , "GT" ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GF" ] ; sld:items xsd:string ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "filter AnnotSV tsv output generated from a bcftools merged vcf" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "python3" "AnnotSV_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:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "import argparse\nimport csv\nimport sys\n\nparser = argparse.ArgumentParser()\nparser.add_argument('--input', '-i', dest=\"input\", help='input AnnotSV tsv file', required=True, action=\"store\")\nparser.add_argument('--output', '-o', dest=\"output\", help='output tsv file name', required=True, action=\"store\")\nparser.add_argument('--filtering_frequency', dest=\"filtering_frequency\", help=\"frequency to filter with\", action=\"store\", type=float, default=\"0.05\")\nparser.add_argument('--all-CDS', dest=\"CDS\", help=\"Do not require a positive CoDing Sequence overlap\", action=\"store_true\")\nparser.add_argument('--ignore-pass-filter', dest=\"filter\", help=\"Do not require calls to have a PASS filter\", action=\"store_true\")\n\nargs = parser.parse_args()\ninput_file_name = args.input\noutput_file_name = args.output\nfiltering_frequency = args.filtering_frequency\nall_cds = args.CDS\nignore_pass_filter = args.filter\n\nwith open(input_file_name, 'r') as file_in, open(output_file_name, 'w') as file_out:\n file_in = csv.DictReader(file_in, delimiter='\\t')\n file_out = csv.DictWriter(file_out, fieldnames=file_in.fieldnames, delimiter='\\t')\n file_out.writeheader()\n total_sv_count = 0\n pass_sv_count = 0\n for row in file_in:\n total_sv_count += 1\n if(row['AnnotSV type'] == 'split' \\\n and (row['FILTER'] == 'PASS' or ignore_pass_filter) \\\n and (int(row['CDS length']) > 0 or all_cds) \\\n and float(row['IMH_AF']) < filtering_frequency\n and float(row['1000g_max_AF']) < filtering_frequency\n and not(float(row['DGV_LOSS_Frequency']) > filtering_frequency and 'DEL' in row['SV type']) \n and not(float(row['DGV_GAIN_Frequency']) < filtering_frequency and ('DUP' in row['SV type'] or 'INS' in row['SV type']))\n and not(('Manta' in row['ID'] and 'IMPRECISE' in row['INFO']) or (row['QUAL'] != '.' and 'IMPRECISE' in row['INFO'])) ):\n file_out.writerow(row)\n pass_sv_count += 1\n print(\"total sv count:\",total_sv_count)\n print(\"total sv passed count:\",pass_sv_count)\n" ; cwl:entryname "AnnotSV_filter.py" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "python:3" ] . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/bin/python" "/usr/local/bin/cnvkit.py" "batch" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs , , , , , , , , , , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ; ResourceRequirement:tmpdirMin 10000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "etal/cnvkit:0.9.5" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputSource ; sld:type cwl:File . sld:type xsd:double , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , , , ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "Coding Variant filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(inputs.vcf.path)" ] [ cwl:valueFrom "$(runtime.outdir)/annotated.coding_variant_filtered.vcf" ] "/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.coding_variant_filtered.vcf" ] "--ontology" "--filter" "Consequence is coding_sequence_variant" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/vcf_check.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/vep_helper-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . sld:type xsd:string . sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).cram" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ; sld:type cwl:File . sld:type xsd:string . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "method used to merge allow multiallelic indels/snps" ; cwl:default "none" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--merge" ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] . rdfs:comment "Require merged SVs to be of the same type" ; cwl:inputBinding [ CommandLineBinding:position 4 ; cwl:valueFrom "${\n if(inputs.same_type){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n" ] ; sld:type xsd:boolean . sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; sld:type cwl:File . cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:run . cwl:source . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:default "filtered_cnvnator.vcf" . rdfs:comment "output file name" ; cwl:default "AnnotSV.tsv" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-outputFile" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-outputFile" ] ; sld:type xsd:string , sld:null . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default "filtered_smoove.vcf" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot)-scatter.pdf" ] ; sld:type cwl:File , sld:null . sld:type [ sld:items ; sld:type sld:array ] . cwl:source , , . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "bwa-indexed reference file" ; sld:type xsd:string . cwl:default false . sld:type xsd:boolean . cwl:in ; cwl:out ; cwl:run . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . 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:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; 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 ; 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: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: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: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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.file.basename).gz" . cwl:default "ID" , "ALT" , "CHROM" , "POS" , "REF" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "samtools index cram" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.cram.basename)" "$(runtime.outdir)/$(inputs.cram.basename).crai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.cram.basename).crai" "$(runtime.outdir)/$(inputs.cram.nameroot).crai" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.cram; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--ignore-pass-filter" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "Set up and execute manta" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position -1 ; CommandLineBinding:prefix "--runDir" ; cwl:valueFrom "$(runtime.outdir)" ] [ CommandLineBinding:shellQuote false ; cwl:valueFrom "&&" ] "/usr/bin/python" "runWorkflow.py" "-m" "local" [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-j" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/usr/bin/python" "/usr/bin/manta/bin/configManta.py" ) ; 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:ResourceRequirement ; ResourceRequirement:coresMin 12 ; ResourceRequirement:ramMin 24000 ; ResourceRequirement:tmpdirMin 10000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/manta_somatic-cwl:1.5.0" ] . cwl:outputSource ; sld:type cwl:File . sld:type xsd:double , sld:null . sld:type xsd:string . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "annotated.coding_variant_filtered.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 7 ; cwl:valueFrom "${\n if (inputs.custom_clinvar_vcf) {\n return [\"--custom\", inputs.custom_clinvar_vcf.path + \",clinvar,vcf,exact,0,CLINSIGN,PHENOTYPE,SCORE,RCVACC,TESTEDINGTR,PHENOTYPELIST,NUMSUBMIT,GUIDELINES\"]\n\n }\n else {\n return []\n }\n}\n" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . rdfs:comment "Minimum size of SVs to merge" ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; sld:type xsd:int . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , , , . cwl:inputBinding [ CommandLineBinding:prefix "-1" ] ; sld:type cwl:File , sld:null . cwl:in , , , , , , ; cwl:out , , , , ; cwl:run . cwl:source . cwl:in , , , , , , , , , , ; cwl:out ; cwl:run . cwl:source . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: 'homo_sapiens' or 'mus_musculus'" ; cwl:inputBinding [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "--species" ] ; sld:type xsd:string . cwl:source . rdfs:label "a file with a label" ; sld:fields , ; sld:type sld:record . sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "--assembly" ] ; sld:type xsd:string . a cwl:ExpressionTool ; ExpressionTool:expression "${\n var metrics = inputs.verify_bam_id_metrics.contents.split(\"\\n\");\n if ( metrics[0].split(\"\\t\")[6] == 'FREEMIX' ) {\n return {'freemix_score': metrics[1].split(\"\\t\")[6]};\n } else {\n return {'freemix_score:': null };\n }\n}\n" ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_depth.sh" ) ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_depth.sh" ) ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_depth.sh" ) ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_depth.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nINPUT_VCF=\"$1\"\nOUTPUT_VCF=\"$2\"\nDEL_DEPTH=\"$3\"\nDUP_DEPTH=\"$4\"\nVCF_SOURCE=\"$5\"\n\nif [ \"$VCF_SOURCE\" == \"cnvnator\" ]; then\n echo \"Running filter for cnvnator vcf\"\n filter_expression=\"(natorRD>$DUP_DEPTH | natorRD<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"cnvkit\" ]; then\n echo \"Running filter for cnvkit vcf\"\n filter_expression=\"(FOLD_CHANGE>$DUP_DEPTH | FOLD_CHANGE<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"duphold\" ]; then\n echo \"Running filter for vcf annotated by duphold\"\n filter_expression=\"((SVTYPE='DEL' & FMT/DHFFC[0] < $DEL_DEPTH) | (SVTYPE='DUP' & FMT/DHBFC[0] > $DUP_DEPTH) | SVTYPE='BND' | SVTYPE='INS' | SVTYPE='INV')\"\nelse\n echo \"vcf source: '$VCF_SOURCE' is not supported for SV filtering\"\n exit 1\nfi\n/opt/bcftools/bin/bcftools filter \"$INPUT_VCF\" -o \"$OUTPUT_VCF\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_depth.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nINPUT_VCF=\"$1\"\nOUTPUT_VCF=\"$2\"\nDEL_DEPTH=\"$3\"\nDUP_DEPTH=\"$4\"\nVCF_SOURCE=\"$5\"\n\nif [ \"$VCF_SOURCE\" == \"cnvnator\" ]; then\n echo \"Running filter for cnvnator vcf\"\n filter_expression=\"(natorRD>$DUP_DEPTH | natorRD<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"cnvkit\" ]; then\n echo \"Running filter for cnvkit vcf\"\n filter_expression=\"(FOLD_CHANGE>$DUP_DEPTH | FOLD_CHANGE<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"duphold\" ]; then\n echo \"Running filter for vcf annotated by duphold\"\n filter_expression=\"((SVTYPE='DEL' & FMT/DHFFC[0] < $DEL_DEPTH) | (SVTYPE='DUP' & FMT/DHBFC[0] > $DUP_DEPTH) | SVTYPE='BND' | SVTYPE='INS' | SVTYPE='INV')\"\nelse\n echo \"vcf source: '$VCF_SOURCE' is not supported for SV filtering\"\n exit 1\nfi\n/opt/bcftools/bin/bcftools filter \"$INPUT_VCF\" -o \"$OUTPUT_VCF\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_depth.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nINPUT_VCF=\"$1\"\nOUTPUT_VCF=\"$2\"\nDEL_DEPTH=\"$3\"\nDUP_DEPTH=\"$4\"\nVCF_SOURCE=\"$5\"\n\nif [ \"$VCF_SOURCE\" == \"cnvnator\" ]; then\n echo \"Running filter for cnvnator vcf\"\n filter_expression=\"(natorRD>$DUP_DEPTH | natorRD<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"cnvkit\" ]; then\n echo \"Running filter for cnvkit vcf\"\n filter_expression=\"(FOLD_CHANGE>$DUP_DEPTH | FOLD_CHANGE<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"duphold\" ]; then\n echo \"Running filter for vcf annotated by duphold\"\n filter_expression=\"((SVTYPE='DEL' & FMT/DHFFC[0] < $DEL_DEPTH) | (SVTYPE='DUP' & FMT/DHBFC[0] > $DUP_DEPTH) | SVTYPE='BND' | SVTYPE='INS' | SVTYPE='INV')\"\nelse\n echo \"vcf source: '$VCF_SOURCE' is not supported for SV filtering\"\n exit 1\nfi\n/opt/bcftools/bin/bcftools filter \"$INPUT_VCF\" -o \"$OUTPUT_VCF\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_depth.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nINPUT_VCF=\"$1\"\nOUTPUT_VCF=\"$2\"\nDEL_DEPTH=\"$3\"\nDUP_DEPTH=\"$4\"\nVCF_SOURCE=\"$5\"\n\nif [ \"$VCF_SOURCE\" == \"cnvnator\" ]; then\n echo \"Running filter for cnvnator vcf\"\n filter_expression=\"(natorRD>$DUP_DEPTH | natorRD<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"cnvkit\" ]; then\n echo \"Running filter for cnvkit vcf\"\n filter_expression=\"(FOLD_CHANGE>$DUP_DEPTH | FOLD_CHANGE<$DEL_DEPTH)\"\nelif [ \"$VCF_SOURCE\" == \"duphold\" ]; then\n echo \"Running filter for vcf annotated by duphold\"\n filter_expression=\"((SVTYPE='DEL' & FMT/DHFFC[0] < $DEL_DEPTH) | (SVTYPE='DUP' & FMT/DHBFC[0] > $DUP_DEPTH) | SVTYPE='BND' | SVTYPE='INS' | SVTYPE='INV')\"\nelse\n echo \"vcf source: '$VCF_SOURCE' is not supported for SV filtering\"\n exit 1\nfi\n/opt/bcftools/bin/bcftools filter \"$INPUT_VCF\" -o \"$OUTPUT_VCF\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_depth.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).CNVnator.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--filtering_frequency" ] ; sld:type xsd:double , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string , sld:null . sld:type xsd:string . sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_name)" ] ; sld:type cwl:File . 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: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 ; 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 ; 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: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: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: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:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).root" ] ; sld:type cwl:File . rdfs:comment "output vcf file name" ; cwl:default "duphold_annotated.vcf" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--output" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--output" ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "add VEP annotation to report" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ] ) ; cwl:baseCommand ( "vep-annotation-reporter" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] . cwl:source . rdfs:comment "output vcf file name" ; cwl:default "filtered_sv.vcf" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\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:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name).merged.bam" ] ; sld:type cwl:File . cwl:valueFrom "${ if (inputs.intervals.length == 1 && inputs.intervals[0].match(/^[0-9A-Za-z]+$/)) { return inputs.intervals[0] + \".g.vcf.gz\"; } else { return \"output.g.vcf.gz\"; } }" . cwl:source . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--coding_only" ] ; sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . rdfs:comment "snps vcf(s) for adding hom/het snp counts found within svs" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 5 ; CommandLineBinding:prefix "-vcfFiles" ] ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 5 ; CommandLineBinding:prefix "-vcfFiles" ] ; sld:type sld:null ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , , , ; cwl:out ; cwl:run . rdfs:comment "ensembl version - Must be present in the cache directory. Example: '95'" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "--cache_version" ] ; sld:type xsd:string . sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "merge" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "create BQSR table" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/bqsr.table" ] "--preserve_qscores_less_than" "6" "--disable_auto_index_creation_and_locking_when_reading_rods" "--disable_bam_indexing" "-dfrac" ".1" "-nct" "4" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "BaseRecalibrator" ) ; 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 18000 ] . cwl:in , , ; cwl:out , ; cwl:run . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type xsd:int , sld:null . a cwl:Workflow ; rdfs:label "wgs alignment with qc" ; 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:SchemaDefRequirement ; SchemaDefRequirement:types , ] . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/diploidSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).GcBiasMetrics.txt" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Used for naming the output file" ; cwl:default "SV" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--name" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-r" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:default true . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).WgsMetrics.txt" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; sld:type xsd:boolean , sld:null . sld:fields , ; sld:type sld:record . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Mark duplicates and Sort" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position 4 ; cwl:valueFrom "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ) ; cwl:baseCommand ( "/bin/bash" "markduplicates_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\ndeclare MD_BARCODE_TAG\nif [ ! -z \"$6\" ]; then\n MD_BARCODE_TAG=\"BARCODE_TAG=$6\"\n/usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT \"$MD_BARCODE_TAG\" | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nelse\n /usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nfi\n" ; cwl:entryname "markduplicates_helper.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mark_duplicates-cwl:1.0.1" ] . cwl:in ; cwl:out ; cwl:run . cwl:source . rdfs:comment "Depth for deletions must be less than this cutoff to pass the filter." ; cwl:default 7.5e-01 ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:double , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -4 ; CommandLineBinding:prefix "--referenceFasta" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "vcf file to filter" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "Used to generate the output file name" ; cwl:default "SURVIVOR-sv-merged.vcf" ; cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type xsd:boolean . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , , ; cwl:out , , , , , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--tumorBam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "Filter single sample sv vcf from depth callers(cnvkit/cnvnator)" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , ; cwl:outputs . sld:type xsd:boolean , sld:null . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:in , , , , ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . cwl:default "select_variants" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type xsd:double , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).CNVnator.cn" ] ; sld:type cwl:File . sld:type xsd:boolean . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "cnvkit.vcf" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:double , sld:null . sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:comment "Due to workflow runner limitations, use sequence_align_and_tag_adapter.cwl subworkflow to call this" ; rdfs:label "align with bwa_mem and tag" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-n" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/bin/bash" "sequence_alignment_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 20000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/alignment_helper-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\nset -o nounset\n\nwhile getopts \"b:?1:?2:?g:r:n:\" opt; do\n case \"$opt\" in\n b)\n MODE=bam\n BAM=\"$OPTARG\"\n ;;\n 1)\n MODE=fastq\n FASTQ1=\"$OPTARG\"\n ;;\n 2) \n MODE=fastq\n FASTQ2=\"$OPTARG\"\n ;;\n g)\n READGROUP=\"$OPTARG\"\n ;;\n r)\n REFERENCE=\"$OPTARG\"\n ;;\n n)\n NTHREADS=\"$OPTARG\"\n ;;\n esac\ndone\n\nif [[ \"$MODE\" == 'fastq' ]]; then\n /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -R \"$READGROUP\" \"$REFERENCE\" \"$FASTQ1\" \"$FASTQ2\" | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\nfi\nif [[ \"$MODE\" == 'bam' ]]; then\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\nfi\n" ; cwl:entryname "sequence_alignment_helper.sh" ] ] ; cwl:stdout "refAlign.bam" . cwl:source . cwl:default "final" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . rdfs:comment "bwa-indexed reference file" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-r" ] ; sld:type xsd:string . cwl:in , , , , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--variant" ] ; sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . sld:type xsd:string . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:in , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , ; cwl:run . sld:type sld:null ; sld:type [ sld:symbols , , , ; sld:type sld:enum ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File . cwl:in , , , , , , ; cwl:out ; cwl:run . sld:type xsd:string . sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . rdfs:comment "if present in variant, number of alternate split reads support needed to pass" ; cwl:default 2 ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:int , sld:null . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Ensembl Variant Effect Predictor" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--format" "vcf" "--vcf" "--fork" "4" "--term" "SO" "--transcript_version" "--offline" "--cache" "--symbol" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:1.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 64000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:double , sld:null . cwl:secondaryFiles [] ; sld:type [ cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-knownSites" ] ; sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "annotated.vcf" ] ; sld:type cwl:File . cwl:source . rdfs:label "sequence data with readgroup information" ; sld:fields , ; sld:type sld:record . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "collect HS metrics" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:in , , , ; cwl:out , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).cnr" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Bin size used to calculate coverage" ; cwl:default 100 ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:int , sld:null . rdfs:comment "Sample name used for output file naming" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . cwl:default "final" ; sld:type xsd:string , sld:null . sld:type xsd:int . cwl:source . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_read_support.sh" ) ; cwl:baseCommand ( "/bin/bash" "filter_sv_vcf_read_support.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nabundance=\"$1\"\ninput_vcf=\"$2\"\noutput_vcf=\"$3\"\npaired_count=\"$4\"\nsplit_count=\"$5\"\nvcf_source=\"$6\"\n\nif [ \"$vcf_source\" == \"smoove\" ]; then\n echo \"Running filter for smoove vcf\"\n filter_expression=\"((AS >= $split_count) && (AP >= $paired_count) && ((AP+AS) / (AP+RP+AS+RS) >= $abundance))\"\nelif [ \"$vcf_source\" == \"manta\" ]; then\n echo \"Running filter for manta vcf\"\n filter_expression=\"((SR[0:*]=\\\".\\\" || (SR[0:1] >= $split_count)) && (PR[0:1] >= $paired_count) && ((SR[0:*]=\\\".\\\" && (PR[0:1] / (PR[0:0]+PR[0:1]) >= $abundance))|| ((SR[0:1]+PR[0:1]) / (SR[0:0]+SR[0:1]+PR[0:1]+PR[0:0]) >= $abundance)))\"\nelse\n echo \"vcf source: '$vcf_source' is not supported for SV filtering\"\n exit 1\nfi\n\n/opt/bcftools/bin/bcftools filter \"$input_vcf\" -o \"$output_vcf\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_read_support.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\n\nabundance=\"$1\"\ninput_vcf=\"$2\"\noutput_vcf=\"$3\"\npaired_count=\"$4\"\nsplit_count=\"$5\"\nvcf_source=\"$6\"\n\nif [ \"$vcf_source\" == \"smoove\" ]; then\n echo \"Running filter for smoove vcf\"\n filter_expression=\"((AS >= $split_count) && (AP >= $paired_count) && ((AP+AS) / (AP+RP+AS+RS) >= $abundance))\"\nelif [ \"$vcf_source\" == \"manta\" ]; then\n echo \"Running filter for manta vcf\"\n filter_expression=\"((SR[0:*]=\\\".\\\" || (SR[0:1] >= $split_count)) && (PR[0:1] >= $paired_count) && ((SR[0:*]=\\\".\\\" && (PR[0:1] / (PR[0:0]+PR[0:1]) >= $abundance))|| ((SR[0:1]+PR[0:1]) / (SR[0:0]+SR[0:1]+PR[0:1]+PR[0:0]) >= $abundance)))\"\nelse\n echo \"vcf source: '$vcf_source' is not supported for SV filtering\"\n exit 1\nfi\n\n/opt/bcftools/bin/bcftools filter \"$input_vcf\" -o \"$output_vcf\" -i \"$filter_expression\"\n" ; cwl:entryname "filter_sv_vcf_read_support.sh" ] ] . cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:default "final" ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "required alternate read abundance percentage to pass" ; cwl:default 1e-01 ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:double , sld:null . a cwl:CommandLineTool ; rdfs:label "Run Smoove v0.1.6" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "call" "--processes" "4" "-F" ) ; cwl:baseCommand ( "/usr/local/bin/smoove" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 20000 ; ResourceRequirement:tmpdirMin 10000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "brentp/smoove@sha256:9d5098d3882df1443aae36922d36b5188af1cb9b8f83dab4a9ed041a6a8019cc" ] . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-g" ] ; sld:type xsd:string . rdfs:comment "BAM or CRAM input" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . rdfs:comment "input bgzipped tabix indexed vcfs to merge" ; cwl:inputBinding [ CommandLineBinding:position 6 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; sld:type cwl:File . cwl:valueFrom "ALL_READS" . sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/candidateSmallIndels.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:boolean , sld:null . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:comment "Some workflow engines won't stage files in our nested structure, so parse it out here" ; rdfs:label "adapter for sequence_align_and_tag" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:default "hybrid" ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--method" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-genomeBuild" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-genomeBuild" ] ; sld:type xsd:string . sld:type cwl:File . rdfs:comment "the unaligned sequence data with readgroup information" ; sld:type . cwl:source . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--all-CDS" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . rdfs:comment "Array of VCFs to merge SV calls of" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(self.readgroup)" . rdfs:comment "aligned bam/cram file" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--bam" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--bam" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:valueFrom "ALL_READS" . cwl:default true . cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; sld:type cwl:File . cwl:in , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . sld:type [ sld:items ; sld:type sld:array ] . cwl:in , , , , ; cwl:out ; cwl:run . rdfs:comment "resolve duplicate sample names" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--force-samples" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . rdfs:comment "assume genotypes at missing sites are 0/0" ; cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--missing-to-ref" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "array of plugins to use when running vep" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:default "out" ; sld:type xsd:string , sld:null . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:source . cwl:default "duphold" . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--access" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "reference used to align bam" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--fasta" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string .