@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:in , , , , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . rdfs:comment "Array of VCFs to merge SV calls of" ; cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . rdfs:comment "Maximum distance of variants to consider for merging" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:int . a cwl:CommandLineTool ; rdfs:label "add population allele frequencies to a vcf" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/opt/hall-lab/python-2.7.15/bin/svtools" "afreq" "$(inputs.vcf)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/opt/hall-lab/python-2.7.15/bin/svtools" "vcftobedpe" "-i" "stdin" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/opt/hall-lab/python-2.7.15/bin/svtools" "varlookup" "-d" "200" "-c" "POPFREQ" "-a" "stdin" "-b" "$(inputs.sv_db)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/opt/hall-lab/python-2.7.15/bin/svtools" "bedpetovcf" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "halllab/svtools:v0.4.0-2dc7f91" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 5000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:stdout "$(inputs.cohort_name)" . cwl:source . cwl:source . cwl:in ; cwl:out , ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "target-$(self.label)" . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . 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:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . sld:type xsd:boolean . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--normal" ] ; sld:type cwl:File , sld:null . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position -4 ; CommandLineBinding:prefix "--referenceFasta" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somaticSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . sld:type xsd:string . rdfs:comment "BAM/BED/GFF/VCF file to compare to file b" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-a" ] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:default "Wildtype" , "Downstream" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type cwl:File , sld:null . cwl:source . 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] . cwl:outputSource ; sld:type cwl:File . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--coding_only" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--coding_only" ] ; sld:type xsd:boolean . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "--centerReads" ] ; sld:type xsd:boolean , sld:null . cwl:source . sld:type xsd:int . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:in , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:in , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , , , ; cwl:run . 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).targetcoverage.cnn" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "annotated.max_sv_pf_filtered.vcf" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "summary-$(self.label)" . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "GcBiasMetricsSummary.txt" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "samtools flagstat" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "flagstat" ) ; 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/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.bam.basename).flagstat" . cwl:default "hybrid" ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--method" ] ; sld:type xsd:string , sld:null . sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , ; cwl:out , , , , ; cwl:run . cwl:source . 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:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . sld:type xsd:boolean , sld:null . cwl:source . cwl:default false . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-contamination" ] ; sld:type xsd:string , sld:null . cwl:in , , , , , , , , , , , , ; cwl:out , ; cwl:run . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/intervals_to_bed.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/perl_helper-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "interval_list.bed" . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type xsd:string . cwl:source . cwl:source . cwl:default "MT" , "X" , "Y" ; cwl:inputBinding [ CommandLineBinding:prefix "-ignore" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . a cwl:Workflow ; rdfs:label "Unaligned to aligned BAM" ; 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:source . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:default "MarkedSorted.bam" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . 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:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.5.0" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; sld:type xsd:string . cwl:in , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "bqsr.table" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "$(self.file)" . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:in , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:default "out" ; sld:type xsd:string , sld:null . cwl:source . sld:type xsd:boolean , sld:null . cwl:source . 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:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 2000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/survivor-cwl:1.0.6.2" ] . sld:type xsd:boolean , sld:null . sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . 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 "$(inputs.male_reference)" ] "-o" "adjusted.tumor.cns" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "&&" ] "/usr/bin/python" "/usr/local/bin/cnvkit.py" "export" "vcf" "adjusted.tumor.cns" ) ; cwl:baseCommand ( "/usr/bin/python" "/usr/local/bin/cnvkit.py" "call" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "etal/cnvkit:0.9.5" ] . cwl:source . cwl:source . cwl:source . sld:type xsd:int , sld:null . cwl:source . rdfs:comment "Reference used to generate the bams" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\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:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\n if (inputs.custom_gnomad_vcf) {\n return ['--check_existing', '--custom', inputs.custom_gnomad_vcf.path + ',gnomADe,vcf,exact,0,AF,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH,AF_SAS']\n }\n else {\n return []\n }\n}\n" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-b" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(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).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; sld:type cwl:File , sld:null . cwl:default "flag_pick" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--" ; CommandLineBinding:separate false ] ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--" ; CommandLineBinding:separate false ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . sld:type xsd:string . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:outputSource ; sld:type cwl:File . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . sld:type xsd:boolean . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "WgsMetrics.txt" ] ; sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.selfSM" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--ignoreDuplicates" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string . cwl:source . cwl:default false . sld:type xsd:boolean , sld:null . cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-ERC" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "interval_list.bed" ] ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:source . sld:type xsd:string . cwl:source . a cwl:CommandLineTool ; rdfs:label "collect alignment summary metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "OUTPUT=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "verify BAM ID" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--out" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).VerifyBamId" ] ) ; cwl:baseCommand ( "/usr/local/bin/verifyBamID" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/verify_bam_id-cwl:1.1.3" ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source ; cwl:valueFrom "intersect-$(self.label).vcf" . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--maxFragmentLength" ] ; sld:type xsd:int , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:default true . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--everything" ] ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--everything" ] ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . rdfs:comment "Require merged SVs to be of the same type" ; cwl:inputBinding [ CommandLineBinding:position 4 ; cwl:valueFrom "${\n if(inputs.same_type){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n" ] ; sld:type xsd:boolean . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/tumorSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:string . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).cram" ] ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot)-scatter.pdf" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cohort_name)" ] ; sld:type cwl:File . sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "Samtools: merge" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(inputs.name).merged.bam" ) ; 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:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 8000 ] . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type xsd:boolean , sld:null . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , ; cwl:out , ; cwl:run . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; sld:type xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:float , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type xsd:string , 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:source . 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 . 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:DockerRequirement ; DockerRequirement:dockerPull "brentp/smoove@sha256:9d5098d3882df1443aae36922d36b5188af1cb9b8f83dab4a9ed041a6a8019cc" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 20000 ; ResourceRequirement:tmpdirMin 10000 ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; sld:type xsd:string . cwl:source . cwl:source . sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GQB" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:default 1e-01 ; sld:type xsd:float , sld:null . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cram.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:float . cwl:inputBinding [ CommandLineBinding:prefix "-bl" ] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "collect WGS metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/WgsMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectWgsMetrics" ) ; 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 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Minimum number of sv calls needed to be merged" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:int . sld:type xsd:boolean . cwl:source . cwl:default "bigwig" ; cwl:inputBinding [ CommandLineBinding:prefix "-of" ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File , sld:null . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cohort_name)-smoove.genotyped.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--scatter" ] ; sld:type xsd:boolean , sld:null . a cwl:CommandLineTool ; rdfs:label "deepTools bamCoverage" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" "$(inputs.bam.basename).$(inputs.outfile_format)" "-p" "$(runtime.cores)" ) ; cwl:baseCommand ( "/usr/local/bin/bamCoverage" ) ; 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 "quay.io/biocontainers/deeptools:3.1.3--py35h470a237_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 32000 ] . cwl:source . rdfs:comment "Bed file used to exclude regions" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--exclude" ] ; sld:type cwl:File , sld:null . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:int , sld:null . sld:type xsd:boolean , sld:null . cwl:source . cwl:in , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:default true . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name).merged.bam" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\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:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type xsd:string , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:source . 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:default "final.bam" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position -2 ; CommandLineBinding:prefix "--normalBam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . cwl:source . cwl:valueFrom "${ if (inputs.intervals.length == 1 && inputs.intervals[0].match(/^[0-9A-Za-z]+$/)) { return inputs.intervals[0] + \".g.vcf.gz\"; } else { return \"output.g.vcf.gz\"; } }" . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "GcBiasMetrics.txt" ] ; sld:type cwl:File . sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/diploidSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "Ensembl Variant Effect Predictor" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--format" "vcf" "--vcf" "--fork" "4" "--term" "SO" "--transcript_version" "--offline" "--cache" "--symbol" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.vcf" ] ) ; cwl:arguments ( "--format" "vcf" "--vcf" "--fork" "4" "--term" "SO" "--transcript_version" "--offline" "--cache" "--symbol" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:1.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 64000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 64000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:1.1.0" ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . rdfs:label "a file with a label" ; sld:fields , ; sld:type sld:record . cwl:inputBinding [ CommandLineBinding:prefix "INTERVALS=" ] ; sld:type cwl:File . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "vcf index" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(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:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] . cwl: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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; 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:in , , , , , , ; cwl:out , ; cwl:run . 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 . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "bed file containing allele frequencies for a population" ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; cwl:valueFrom "${\n return [\n \"--filter\",\n [\n \"POPFREQ_AF\", \"<\", inputs.maximum_sv_population_frequency,\n \"or not\", \"POPFREQ_AF\"\n ].join(\" \")\n ]\n}\n" ] ; sld:type xsd:float . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).cns" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , , ; cwl:out , , , , , ; cwl:run . cwl:source . sld:type xsd:int . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . sld:type cwl:File . 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)/$(inputs.cram.nameroot).crai" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.cram)" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ; sld:type cwl:File . cwl:source . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . sld:type xsd:boolean . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename).$(inputs.outfile_format)" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--allowMissingData" "-o" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantsToTable" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:default "SYMBOL" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "-v" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . 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 ; 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 10000 ] . cwl:inputBinding [ CommandLineBinding:prefix "--smoothLength" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-r" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:string . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:source . 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 . rdfs:comment "ensembl version - Must be present in the cache directory. Example: '95'" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "--cache_version" ] ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "--cache_version" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).antitargetcoverage.cnn" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-y" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "--minFragmentLength" ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:valueFrom "ALL_READS" . rdfs:comment "Require merged SVs to be on the same strand" ; cwl:inputBinding [ CommandLineBinding:position 5 ; cwl:valueFrom "${\n if(inputs.same_strand){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n" ] ; sld:type xsd:boolean . cwl:default false . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:outputBinding [ CommandOutputBinding:glob "${ \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:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--samFlagExclude" ] ; sld:type xsd:int , sld:null . sld:type xsd:int . cwl:default "select_variants" ; sld:type xsd:string , sld:null . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "SV filtering workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-BQSR" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "collect insert size metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; 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:default false ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-y" ] ; sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--variant" ] ; sld:items cwl:File ; sld:type sld:array ] . 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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/candidateSV.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . 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:inputBinding [ CommandLineBinding:prefix "--skipNAs" ] ; sld:type xsd:boolean , sld:null . sld:type xsd:int , sld:null . sld:type xsd:int , sld:null . 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 ; 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:inputs , , , , , , , , , ; cwl:outputs , , ; 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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--filterRNAstrand" ] ; sld:type sld:null ; sld:type [ sld:symbols , ; sld:type sld:enum ] . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type [ cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-knownSites" ] ; sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:default "output.g.vcf.gz" ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . 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:outputSource ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:valueFrom "ALL_READS" . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/candidateSmallIndels.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . 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 . 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:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source ; cwl:valueFrom "${ \n if(inputs.output_name) {\n return inputs.output_name;\n } \n else {\n return inputs.tumor_bam.nameroot + \".cnvkit.vcf\"\n } \n}\n" . cwl:inputBinding [ CommandLineBinding:prefix "--exactScaling" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type cwl:File , sld:null . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "Write the original entry in A for each overlap, default to true" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-wa" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:default "RPGC" ; cwl:inputBinding [ CommandLineBinding:prefix "--normalizeUsing" ] ; sld:type [ sld:symbols , , , , ; sld:type sld:enum ] . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "refAlign.bam" ] ; sld:type cwl:File . cwl:source . cwl:valueFrom "ALL_READS" . cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source , , . a cwl:CommandLineTool ; rdfs:label "POPFREQ_AF filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(inputs.vcf.path)" ] [ cwl:valueFrom "$(runtime.outdir)/annotated.max_sv_pf_filtered.vcf" ] "/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "--vcf_info_field" "tmp" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.max_sv_pf_filtered.vcf" ] ) ; 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:1.0.1" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--samFlagInclude" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot).cnr" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . sld:type xsd:string , sld:null . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:boolean . cwl:source . cwl:source . cwl:source . sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; sld:type cwl:File . 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: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 ] . sld:type xsd:int . a cwl:ExpressionTool ; ExpressionTool:expression "${\n var metrics = inputs.verify_bam_id_metrics.contents.split(\"\\n\");\n if ( metrics[0].split(\"\\t\")[6] == 'FREEMIX' ) {\n return {'freemix_score': metrics[1].split(\"\\t\")[6]};\n } else {\n return {'freemix_score:': null };\n }\n}\n" ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "--minMappingQuality" ] ; sld:type xsd:int , sld:null . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . sld:type [ sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "--scaleFactor" ] ; sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--tumorBam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "BAM to CRAM conversion" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "view" "-C" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:stdout "$(inputs.bam.nameroot).cram" . cwl:in , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , , , , , ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:linkMerge "merge_flattened" ; cwl:source . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:string , sld:null . sld:type [ sld:items ; sld:type sld:array ] . cwl:default "GT" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . 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:in , ; cwl:out ; cwl:run . cwl:source . 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 . cwl:source . cwl:default "variants" ; sld:type xsd:string , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "create BQSR table" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/bqsr.table" ] "--preserve_qscores_less_than" "6" "--disable_auto_index_creation_and_locking_when_reading_rods" "--disable_bam_indexing" "-dfrac" ".1" "-nct" "4" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "BaseRecalibrator" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:in , , , , , , , , , , , , , , ; cwl:out , , , , ; cwl:run . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:in , , ; cwl:out , ; cwl:run . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . sld:type [ sld:items ; sld:type sld:array ] . sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:source . sld:type cwl:File , sld:null . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "align with bwa_mem and tag" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 4 ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/bin/bash" "/usr/bin/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:DockerRequirement ; DockerRequirement:dockerPull "mgibio/alignment_helper-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 20000 ] ; cwl:stdout "refAlign.bam" . rdfs:comment "vcf to add population allele frequencies to" ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.tumor_bam.nameroot)-diagram.pdf" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "annotated.coding_variant_filtered.vcf" ] ; sld:type cwl:File . cwl:default true ; cwl:inputBinding [ CommandLineBinding:prefix "-e" ] ; sld:type xsd:boolean , sld:null . sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 7 ; cwl:valueFrom "${\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:inputBinding [ CommandLineBinding:position 7 ; cwl:valueFrom "${\n if (inputs.custom_clinvar_vcf) {\n return [\"--custom\", inputs.custom_clinvar_vcf.path + \",clinvar,vcf,exact,0,CLINSIGN,PHENOTYPE,SCORE,RCVACC,TESTEDINGTR,PHENOTYPELIST,NUMSUBMIT,GUIDELINES\"]\n\n }\n else {\n return []\n }\n}\n" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(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 cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default "ID" , "ALT" , "CHROM" , "POS" , "REF" , "set" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . sld:type xsd:boolean . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename).flagstat" ] ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "$(self.label)" . cwl:source . cwl:source . sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--access" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--cnr" ] ; sld:type cwl:File , sld:null . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--dir" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--dir" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:default "hybrid" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:boolean , sld:null . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type xsd:string . cwl:default "queryname" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . cwl:source . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "SEQUENCE_DICTIONARY=" ] ; 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:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/manta_somatic-cwl:1.5.0" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 12 ; ResourceRequirement:ramMin 24000 ; ResourceRequirement:tmpdirMin 10000 ] . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/opt/ccdg/bedtools-2.27.1/bin/bedtools" "intersect" ) ; 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 "ernfrid/bedtools:v2.27.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.output_name)" . sld:type xsd:boolean . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "${\n var glob_base = \".antitargetcoverage.cnn\";\n if (inputs.normal_bam) {\n glob_base = inputs.normal_bam.nameroot + glob_base;\n }\n return glob_base;\n}\n" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-r" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:prefix "-bs" ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string , sld:null . cwl:source . a cwl:Workflow ; rdfs:label "wgs 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 ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cohort_name)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . sld:type xsd:string . cwl:in , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; sld:type xsd:string . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "apply BQSR" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_name)" ] "-preserveQ" "6" "-SQQ" "10" "-SQQ" "20" "-SQQ" "30" "-nct" "8" "--disable_indel_quals" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "PrintReads" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . rdfs:comment "bgzip-compressed, tabix-indexed BED file specifiying regions to which variant analysis will be restricted" ; cwl:inputBinding [ CommandLineBinding:position -5 ; CommandLineBinding:prefix "--callRegions" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . cwl:source . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 9 ] ; cwl:inputBinding [ CommandLineBinding:position 9 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--plugin" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--plugin" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:default "per_gene" . cwl:source . a cwl:CommandLineTool ; rdfs:label "sort BAM by name" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-t" [ cwl:valueFrom "$(runtime.cores)" ] "-m" "12G" "-n" "-o" [ cwl:valueFrom "$(inputs.bam.nameroot).NameSorted.bam" ] ) ; cwl:baseCommand ( "/usr/bin/sambamba" "sort" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/sambamba-cwl:0.6.4" ] . cwl:outputBinding [ CommandOutputBinding:glob "sorted.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "Print the header from the A file prior to results, default to true" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-header" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--synonyms" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--synonyms" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "genotype.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "Consequence" , "Feature" , "SYMBOL" , "HGVSp" , "HGVSc" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.depthSM" ] ; sld:type cwl:File . cwl:source . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "collect gc bias metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/GcBiasMetrics.txt" ] "CHART=" [ cwl:valueFrom "$(runtime.outdir)/GcBiasMetricsChart.pdf" ] "S=" [ cwl:valueFrom "$(runtime.outdir)/GcBiasMetricsSummary.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectGcBiasMetrics" ) ; 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 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . a cwl:Workflow ; rdfs:label "scatter GATK HaplotypeCaller over intervals" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:source , , . cwl:outputSource ; sld:type cwl:File . rdfs:comment "BAM/BED/GFF/VCF file to compare to file a" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-b" ] ; sld:type cwl:File . 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" ] ; cwl:inputBinding [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "--species" ] ; sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run . cwl:source . sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:default "merged_annotated.vcf" ; sld:type xsd:string , sld:null . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "annotated.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in , , , , , , ; cwl:out , , , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).NameSorted.bam" ] ; sld:type cwl:File . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:in , , ; cwl:out , , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-T" ] ; sld:type xsd:string . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "reference.cnn" ] ; sld:type cwl:File , sld:null . cwl:default false . cwl:in , ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "base-$(self.label)" . a cwl:Workflow ; rdfs:label "merge and annotate svs with population allele freq and vep" ; 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 ] . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . 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 ] . cwl:default "chr18" , "chr9" , "chr12" , "chr2" , "chr19" , "chr8" , "chr5" , "chr14" , "chr4" , "chr15" , "chr22" , "chr1" , "chr10" , "chr17" , "chr16" , "chr11" , "chr6" , "chr7" , "chr21" , "chr20" , "chr13" , "chr3" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--diagram" ] ; sld:type xsd:boolean , sld:null . cwl:in , , , , , , , , , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--targets" ] ; sld:type cwl:File , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . rdfs:comment "toggles on settings for WES" ; cwl:inputBinding [ CommandLineBinding:position -6 ; CommandLineBinding:prefix "--exome" ] ; sld:type xsd:boolean , sld:null . cwl:default "Final.bam" ; sld:type xsd:string , sld:null . 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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:1.0.0" ] . cwl:source . rdfs:comment "Minimum size of SVs to merge" ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; sld:type xsd:int . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "annotated.vcf_summary.html" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.vcf_summary.html" ] ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:source . sld:type xsd:string . cwl:source . cwl:in , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--drop-low-coverage" ] ; sld:type xsd:boolean , sld:null . sld:type xsd:string , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "GcBiasMetricsChart.pdf" ] ; sld:type cwl:File . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--dbsnp" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source . sld:type cwl:File , sld:null . 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.bam)" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "Unaligned BAM to BQSR and VCF" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . 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 ] . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--fasta" ] ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--fasta" ] ; sld:type xsd:string , sld:null . sld:type xsd:int . sld:type cwl:File , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File . rdfs:comment "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "--assembly" ] ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "--assembly" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; sld:type xsd:boolean , sld:null . sld:type cwl:File . sld:type xsd:string . cwl:source . a cwl:CommandLineTool ; rdfs:label "Sort VCF" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/sorted.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/picard/picard.jar" "SortVcf" ) ; 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:source ; cwl:valueFrom "$(self.file)" . cwl:outputSource ; sld:type cwl:File . sld:type xsd:boolean , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:in , , , , ; cwl:out ; cwl:run . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; 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:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:default "ALL_READS" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . sld:type xsd:string , sld:null . cwl:default false . cwl:in , , , ; cwl:out ; cwl:run . sld:type [ sld:items ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "bgzip VCF" ; ns1:original_cwlVersion "v1.2" ; 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:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:stdout "$(inputs.file.basename).gz" . cwl:default 2451960000 ; cwl:inputBinding [ CommandLineBinding:prefix "--effectiveGenomeSize" ] ; sld:type xsd:long , sld:null . cwl:in , , , , , , , , , , ; cwl:out , ; cwl:run . 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 "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "--vcf" ] ; sld:type cwl:File . cwl:source . sld:type xsd:int . cwl:default true . cwl:source . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "Write original A entry once if any overlaps found in B, default to true" ; cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-u" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:default "POPFREQ_AF" , "POPFREQ_VarID" , "SVLEN" , "REF" , "CHR2" , "END" , "ALT" , "ID" , "CHROM" , "NSAMP" , "POS" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "Mark duplicates and Sort" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(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" ] .