@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: . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.selfSM" ] ; sld:type cwl:File . sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--allowMissingData" "-o" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:arguments ( "--allowMissingData" "-o" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantsToTable" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantsToTable" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . sld:type xsd:int , sld:null . rdfs:comment "array of plugins to use when running vep" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "-contamination" ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--variant" ] ; sld:items cwl:File ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:source . a cwl:ExpressionTool ; ExpressionTool:expression "${\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:default "MarkedSorted.bam" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:default "Consequence" , "Feature" , "SYMBOL" , "HGVSp" , "HGVSc" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . 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" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:source . rdfs:comment "custom type, check types directory for input format" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:default true . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-2" ] ; sld:type cwl:File , sld:null . 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" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-PerBaseCoverage.txt" ] ; sld:type cwl:File , sld:null . cwl:in , , , , ; cwl:out ; cwl:run . cwl:source . rdfs:label "File to be used for annotation, include index file" ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--plugin" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . 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 ] . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).NameSorted.bam" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . sld:type cwl:File . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "${\n if(self){\n for(var i=0; i cwl:source . cwl:source . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "collect alignment summary metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "OUTPUT=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectAlignmentSummaryMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type sld:null ; sld:type [ rdfs:label "custom type, check types directory for input format" ; cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\n return [self.annotation.check_existing ? '--check_existing' : '',\n '--custom',\n [self.annotation.file.path,\n self.annotation.name,\n self.annotation.data_format,\n self.method,\n self.force_report_coordinates ? 1 : 0,\n self.annotation.vcf_fields ? self.annotation.vcf_fields : ''\n ].filter(String).join(',')\n ].filter(String)\n}\n" ] ; sld:items ; sld:type sld:array ] . 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 "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/bin/bash" "sequence_alignment_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 20000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/alignment_helper-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\nset -o nounset\n\nwhile getopts \"b:?1:?2:?g:r:n:\" opt; do\n case \"$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\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\nfi\n" ; cwl:entryname "sequence_alignment_helper.sh" ] ] ; cwl:stdout "refAlign.bam" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "genotype.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in , ; cwl:out ; cwl:run . 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 "$(runtime.outdir)/annotated.coding_variant_filtered.vcf" ] "--ontology" "--filter" "Consequence is coding_sequence_variant" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/vcf_check.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:1.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . cwl:source , , . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).VerifyBamId.depthSM" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "annotated.af_filtered.vcf" ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . rdfs:comment "custom type, check types directory for input format" ; sld:type [ sld:items ; sld:type sld:array ] . 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: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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . 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:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . rdfs:comment "bwa-indexed reference file" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-r" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "--everything" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . sld:type [ sld:symbols , , ; sld:type sld:enum ] . 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 ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cram.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source ; cwl:valueFrom "summary-$(self.label)" . cwl:source . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_file_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:default 5e-02 ; sld:type xsd:float . cwl:default "final" ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-T" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:string . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: 'homo_sapiens' or 'mus_musculus'" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "--species" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ; cwl:valueFrom "${\n return [\n \"--filter\",\n [\n inputs.field_name, \"<\", inputs.maximum_population_allele_frequency,\n \"or not\", inputs.field_name\n ].join(\" \")\n ]\n}\n" ] ; sld:type xsd:float . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "collect insert size metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] "H=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . cwl:source ; cwl:valueFrom "base-$(self.label)" . 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 "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerTargetCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\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:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . rdfs:label "Annotation file type" ; sld:symbols , , , , ; sld:type sld:enum . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:source . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . rdfs:comment "filters to apply to reads before analysis" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "--read_filter" ] ; sld:type xsd:string , sld:null . sld:type xsd:string , sld:null . rdfs:comment "select only a certain type of variants" ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-selectType" ] ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-selectType" ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , , , , ; sld:type sld:enum ] . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type [ sld:items ; sld:type sld:array ] . 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)/$(inputs.bam.nameroot).bai" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.bam; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--dbsnp" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; 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 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--fasta" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , 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 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "-1" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:in , , , , , , , , , , , , , , , , , ; cwl:out , , , , , ; cwl:run . cwl:valueFrom "roi" . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.readgroup)" . rdfs:label "Force report the overlapping coordinates of custom feature instead of based on the exact coordinates" ; sld:type xsd:boolean . cwl:in , , , , , , ; cwl:out , , , , ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:default "select_variants" ; sld:type xsd:string , sld:null . cwl:default "out" ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type cwl:File . sld:type cwl:File . cwl:default "annotated.filtered.final" . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . a cwl:Workflow ; rdfs:label "Exome QC 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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] . cwl:valueFrom "annotated.filtered.vcf" . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:source . a cwl:Workflow ; rdfs:label "exome 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:SchemaDefRequirement ; SchemaDefRequirement:types , , ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:valueFrom "ALL_READS" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).cram" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "bwa-indexed reference file" ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "refAlign.bam" ] ; sld:type cwl:File . 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 ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] . cwl:default "output.g.vcf.gz" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "-o" ] ; sld:type xsd:string . cwl:in , , , , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.nameroot)_annotated.vcf_summary.html" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in , , , , , , , , , , ; cwl:out , , , , , , , , , , , ; cwl:run . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run . cwl:source . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:fields , , , , , ; sld:type sld:record . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:in , , , , , , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:comment "Renames a file by staging and then `mv`ing it. A workaround for workflow engines that don't support rename.cwl. If running in cwltool, use the other one instead." ; rdfs:label "Staged Renamer" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type . cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; sld:type cwl:File . cwl:in , , ; cwl:out , ; cwl:run . sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.nameroot)_annotated.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-ERC" ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:valueFrom "annotated.filtered.tsv" . cwl:in , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:valueFrom "ALL_READS" . cwl:default false . cwl:source ; cwl:valueFrom "$(self.file)" . a cwl:CommandLineTool ; rdfs:label "create BQSR table" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/bqsr.table" ] "--preserve_qscores_less_than" "6" "--disable_auto_index_creation_and_locking_when_reading_rods" "--disable_bam_indexing" "-dfrac" ".1" "-nct" "4" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "BaseRecalibrator" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] ; sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] ; sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , ; cwl:out ; cwl:run . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "collect HS metrics" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(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: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: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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; 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:StepInputExpressionRequirement ] ; 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:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/picard-cwl:2.18.1" ] . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:in , , , , , , , , , , , , , , ; cwl:out , , , , , , , , , , , , , ; cwl:run . cwl:in , ; cwl:out , ; cwl:run . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:default false . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--dir" ] ; sld:type cwl:Directory , xsd:string . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . rdfs:comment "parameter to pass to the index creator" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--variant_index_parameter" ] ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "type of IndexCreator to use for VCF/BCF indices" ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "--variant_index_type" ] ; sld:type sld:null ; sld:type [ sld:symbols , , , ; sld:type sld:enum ] . cwl:default "Wildtype" , "Downstream" ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . a cwl:Workflow ; rdfs:label "Apply filters to VCF file" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:default true . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . 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:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "annotated.coding_variant_filtered.vcf" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "apply BQSR" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_name).bam" ] "-preserveQ" "6" "-SQQ" "10" "-SQQ" "20" "-SQQ" "30" "-nct" "8" "--disable_indel_quals" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "PrintReads" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--coding_only" ] ; sld:type xsd:boolean . cwl:in , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . rdfs:label "Used as key for new VEP annotation" ; sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "sort BAM by name" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-t" [ cwl:valueFrom "$(runtime.cores)" ] "-m" "22G" "-n" "-o" [ cwl:valueFrom "$(inputs.bam.nameroot).NameSorted.bam" ] ) ; cwl:baseCommand ( "/usr/bin/sambamba" "sort" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; 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 26000 ] . rdfs:label "custom annotation file to be used by vep" ; sld:fields , , ; sld:type sld:record . cwl:inputBinding [ CommandLineBinding:prefix "--vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:default "flag_pick" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--" ; CommandLineBinding:separate false ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . cwl: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=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; sld:type xsd:int , sld:null . rdfs:comment "include genotypes from this sample" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-b" ] ; sld:type cwl:File , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File . 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:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type [ sld:items ; sld:type sld:array ] . cwl:default "ALL_READS" ; sld:type xsd:string . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source ; cwl:valueFrom "$(self.file)" . sld:type xsd:int , sld:null . sld:type cwl:File . sld:type xsd:string . cwl:source . 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)/$(inputs.cram.nameroot).crai" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.cram; delete f.secondaryFiles; return f }" ] ; 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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; 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:source . rdfs:comment "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--assembly" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "bqsr.table" ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . 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" ] . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "the unaligned sequence data with readgroup information" ; sld:type . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:default "ID" , "POS" , "ALT" , "REF" , "CHROM" , "set" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "target-$(self.label)" . rdfs:label "a file with a label" ; sld:fields , ; sld:type sld:record . 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 "$(runtime.outdir)/$(inputs.vcf.nameroot)_annotated.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; 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:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . 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 "$(inputs.bam.basename).flagstat" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "variants" ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GQB" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:in , , , , , , ; cwl:out , ; cwl:run . a cwl:Workflow ; rdfs:label "HS Metrics workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , ; cwl:outputs , , , , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . a cwl:Workflow ; rdfs:label "scatter GATK HaplotypeCaller over intervals" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type xsd:int , sld:null . sld:type xsd:boolean , sld:null . cwl:in , , , ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . rdfs:label "Identify known variants colocated with input variant" ; sld:type xsd:boolean . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ; sld:type cwl:File . sld:type cwl:Directory , xsd:string . a cwl:CommandLineTool ; rdfs:label "Custom allele frequency filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(inputs.vcf.path)" ] [ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ] "/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/vcf_check.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:1.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--bam" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('bam')? self.sequence.bam : null)" . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('fastq2')? self.sequence.fastq2 : null)" . 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:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "-g" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:default "chr14" , "chr22" , "chr17" , "chr4" , "chr8" , "chr19" , "chr13" , "chr16" , "chr3" , "chr1" , "chr7" , "chr21" , "chr12" , "chr6" , "chr18" , "chr15" , "chr5" , "chr2" , "chr10" , "chr9" , "chr20" , "chr11" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-L" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . cwl:source . cwl:default "queryname" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . cwl:source . rdfs:comment "ensembl version - Must be present in the cache directory. Example: '95'" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "--cache_version" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputSource ; 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 xsd:boolean , sld:null . cwl:inputBinding [ cwl:loadContents true ] ; cwl:inputBinding [ cwl:loadContents true ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . sld:fields ; sld:type sld:record . sld:type xsd:int , sld:null . rdfs:label "sequence data with readgroup information" ; sld:fields , ; sld:type sld:record . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-BQSR" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:default "final" ; sld:type xsd:string . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "bgzip VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:stdout "$(inputs.file.basename).gz" . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "add VEP annotation to report" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ] ) ; cwl:baseCommand ( "vep-annotation-reporter" ) ; cwl:baseCommand ( "vep-annotation-reporter" ) ; 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:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . 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 "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; cwl:inputBinding [ CommandLineBinding:prefix "PER_BASE_COVERAGE=" ; cwl:valueFrom "${\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 [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; 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 "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . cwl:default true . sld:type xsd:string , sld:null . cwl:default false . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . 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" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; sld:type cwl:File . cwl:valueFrom "ALL_READS" . cwl:valueFrom "ALL_READS" . 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 "$(inputs.bam.nameroot).cram" . cwl:default "variants" ; sld:type xsd:string , sld:null . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:default false . cwl:default "ID" , "ALT" , "CHROM" , "POS" , "REF" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--synonyms" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type , . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; sld:type cwl:File . sld:type cwl:Directory , xsd:string . cwl:source . cwl:source . cwl:source . cwl:source . sld:type xsd:float . cwl:source . cwl:default "AD" , "AF" , "DP" , "GT" ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GF" ] ; sld:items xsd:string ; sld:type sld:array ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GF" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "Mark duplicates and Sort" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 40000 ] ; 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 $3 /dev/stdin\nfi\n" ; cwl:entryname "markduplicates_helper.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mark_duplicates-cwl:1.0.1" ] . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:label "Use this annotation for gnomad filtering?" ; sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name).merged.bam" ] ; sld:type cwl:File . cwl:source . sld:type xsd:string , sld:null . a cwl:Workflow ; rdfs:label "exome 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:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:default false . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File , sld:null . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename).flagstat" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name).bam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . rdfs:comment "maximum number of alternate alleles to genotype" ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--max_alternate_alleles" ] ; sld:type xsd:int , sld:null . cwl:in , , ; cwl:out ; cwl:run . sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:valueFrom "annotated.filtered.final.tsv" . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('fastq1')? self.sequence.fastq1 : null)" . cwl:source . rdfs:label "List of VCF fields to annotate" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type . sld:type cwl:File . cwl:default false . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "verify BAM ID" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--out" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).VerifyBamId" ] ) ; cwl:baseCommand ( "/usr/local/bin/verifyBamID" ) ; cwl:cwlVersion ; cwl:hints [ a ; 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" ] . sld:fields , ; sld:type sld:record .