@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: . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "BAM to SAM conversion" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(inputs.bam.nameroot).sam" ) ; cwl:baseCommand ( "/usr/local/bin/samtools" "view" "-h" "-o" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] . cwl:in , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . sld:type [ sld:items ; sld:type sld:array ] . cwl:default false . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ; sld:type cwl:File . sld:type , sld:null . sld:type cwl:File . sld:type , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "samtools index" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/local/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)/$(inputs.bam.nameroot).bai" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.bam; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] . a cwl:Workflow ; rdfs:label "Chipseq alignment for nonhuman with qc and creating homer tag directory" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , , , , , , , , , , , , , , , , ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , , ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . 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 . rdfs:comment "Minimum mapping quality for a read to contribute coverage." ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source ; cwl:valueFrom "$(self.readgroup)" . cwl:outputSource ; sld:type cwl:File . rdfs:label "trimming adapter file and parameters" ; sld:fields , ; sld:type sld:record . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ cwl:valueFrom "$( ['-t', self.adapters.path, '-o', self.min_overlap] )" ] ; sld:type , sld:null . cwl:default false . cwl:source . cwl:source . cwl:source . 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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] . cwl:in , , ; cwl:out , ; cwl:run . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; sld:type cwl:File . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename).flagstat" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:fields ; sld:type sld:record . a cwl:Workflow ; rdfs:label "WGS QC workflow nonhuman" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , ; cwl:outputs , , , , , , , , , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] . sld:type [ sld:items ; sld:type sld:array ] . rdfs:comment "Fasta file with adapters for removal that may contain N." ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:in , ; cwl:out , ; cwl:run . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "METRIC_ACCUMULATION_LEVEL=" ] ; sld:type xsd:string . cwl:valueFrom "ALL_READS" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "homer_tag_directory" ] ; sld:type cwl:Directory . cwl:source . sld:type xsd:int , sld:null . 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:outputBinding [ CommandOutputBinding:glob "refAlign.bam" ] ; sld:type cwl:File . 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 "broadinstitute/picard:2.23.6" ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).GcBiasMetrics.txt" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . a cwl:CommandLineTool ; rdfs:label "collect insert size metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] "H=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).InsertSizeHistogram.pdf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectInsertSizeMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-r" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default "final.bam" ; sld:type xsd:string . cwl:default "merged.bam" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-n" ] ; sld:type xsd:string , sld:null . rdfs:comment "Minimum base quality for a base to contribute coverage. (N bases are considered to have negative infinite quality and will be excluded regardless of this value.)" ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; sld:type xsd:int , sld:null . cwl:default "queryname" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . cwl:source . cwl:valueFrom "ALL_READS" . cwl:source . cwl:source . sld:type cwl:File . cwl:source . cwl:source . cwl:source ; cwl:valueFrom "base-$(self.label)" . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Minimum overlap for removal without pair overlap." ; sld:type xsd:int . sld:type xsd:string , sld:null . cwl:default "false" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-s" ] ; sld:type xsd:boolean , sld:null . cwl:source . cwl:default "final" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . 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 xsd:int , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source ; cwl:valueFrom "target-$(self.label)" . sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:label "a file with a label" ; sld:fields , ; sld:type sld:record . cwl:outputSource ; sld:type cwl:File . rdfs:comment "the unaligned sequence data with readgroup information" ; sld:type . cwl:outputBinding [ CommandOutputBinding:glob "$(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).$(inputs.output_prefix)-PerTargetCoverage.txt" ] ; sld:type cwl:File , sld:null . cwl:default "MarkedSorted.bam" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string , sld:null . cwl:source . cwl:in , , , , , , , ; cwl:out , , , , , , , , , , , , , ; cwl:run . rdfs:comment "bwa-indexed reference file" ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "PER_TARGET_COVERAGE=" ; cwl:valueFrom "${\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:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . sld:type [ sld:items ; sld:type sld:array ] . cwl:default false . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:label "Sambamba: merge" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-t" "$(runtime.cores)" ) ; cwl:baseCommand ( "/bin/bash" "merge.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -o pipefail\nset -o errexit\nset -o nounset\n\nSORTED=false\n\nwhile getopts \"t:n:s:\" opt; do\n case \"$opt\" in\n t)\n NTHREADS=\"$OPTARG\"\n ;;\n n)\n OUTFILENAME=\"$OPTARG\"\n ;;\n s)\n SORTED=true\n ;;\n esac\ndone\n\nBAMS=(\"${@:$OPTIND}\")\nNUM_BAMS=${#BAMS[@]}\n\n#if there is only one bam, just copy it and index it\nif [[ $NUM_BAMS -eq 1 ]]; then\n cp \"$BAMS\" \"$OUTFILENAME\";\nelse\n if [[ $SORTED == \"true\" ]];then\n /usr/bin/sambamba merge -t \"$NTHREADS\" \"$OUTFILENAME\" \"${BAMS[@]}\"\n else #unsorted bams, use picard\n args=(OUTPUT=\"$OUTFILENAME\" ASSUME_SORTED=true USE_THREADING=true SORT_ORDER=unsorted VALIDATION_STRINGENCY=LENIENT)\n for i in \"${BAMS[@]}\";do\n args+=(\"INPUT=$i\")\n done\n java -jar -Xmx6g /opt/picard/picard.jar MergeSamFiles \"${args[@]}\"\n fi\nfi\nif [[ $SORTED == \"true\" ]];then\n /usr/bin/sambamba index \"$OUTFILENAME\"\nfi\n" ; cwl:entryname "merge.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam-merge:0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 8000 ] . cwl:in , , , , , , ; cwl:out , , , , ; cwl:run . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . a cwl:CommandLineTool ; rdfs:label "collect WGS metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).WgsMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectWgsMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "INPUT=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "sort BAM by name" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-t" [ cwl:valueFrom "$(runtime.cores)" ] "-m" "22G" "-n" "-o" [ cwl:valueFrom "$(inputs.bam.nameroot).NameSorted.bam" ] ) ; cwl:baseCommand ( "/usr/bin/sambamba" "sort" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 26000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/sambamba-cwl:0.6.4" ] . cwl:outputSource ; sld:type cwl:Directory . 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 "${\n if(self) {\n return inputs.bam.nameroot + \".\" + inputs.output_prefix + \"-PerBaseCoverage.txt\"\n } else {\n return false;\n }\n}\n" ] ; sld:type xsd:boolean , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:default "out" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_BASE_QUALITY=" ] ; sld:type xsd:int , sld:null . cwl:source . sld:type cwl:File . cwl:source . cwl:default "ALL_READS" ; sld:type xsd:string . rdfs:label "sequence data with readgroup information" ; sld:fields , ; sld:type sld:record . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).GcBiasMetricsChart.pdf" ] ; sld:type cwl:File . sld:type [ sld:items ; sld:type sld:array ] . sld:type [ sld:items ; sld:type sld:array ] . a cwl:Workflow ; rdfs:label "Alignment without 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:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:outputSource ; sld:type cwl:File . rdfs:comment "chipseq_sequence represents the sequencing data as either FASTQs or BAMs with accompanying\nreadgroup information. Note that in the @RG field ID and SM are required.\n" ; rdfs:label "chipseq_sequence: sequencing data and readgroup information" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "MINIMUM_MAPPING_QUALITY=" ] ; sld:type xsd:int , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "REFERENCE_SEQUENCE=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "INTERVALS=" ] ; sld:type cwl:File , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:in , , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:comment "Due to workflow runner limitations, use sequence_align_and_tag_adapter.cwl subworkflow to call this" ; rdfs:label "align with bwa_mem and tag" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-n" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/bin/bash" "sequence_alignment_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\nset -o nounset\n\nRUN_TRIMMING=\"false\"\n\nwhile getopts \"b:?1:?2:?g:r:n:t:?o:?\" 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=\"$OPTARG\"\n ;;\n t)\n RUN_TRIMMING=\"true\"\n TRIMMING_ADAPTERS=\"$OPTARG\"\n ;;\n o)\n RUN_TRIMMING=\"true\"\n TRIMMING_ADAPTER_MIN_OVERLAP=\"$OPTARG\"\n ;;\n esac\ndone\n\nif [[ \"$MODE\" == 'fastq' ]]; then\n if [[ \"$RUN_TRIMMING\" == 'false' ]]; then\n /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -R \"$READGROUP\" \"$REFERENCE\" \"$FASTQ1\" \"$FASTQ2\" | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n else\n /opt/flexbar/flexbar --adapters \"$TRIMMING_ADAPTERS\" --reads \"$FASTQ1\" --reads2 \"$FASTQ2\" --adapter-trim-end LTAIL --adapter-min-overlap \"$TRIMMING_ADAPTER_MIN_OVERLAP\" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads \\\n | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n fi\nfi\nif [[ \"$MODE\" == 'bam' ]]; then\n if [[ \"$RUN_TRIMMING\" == 'false' ]]; then\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n else\n /usr/bin/java -Xmx4g -jar /opt/picard/picard.jar SamToFastq I=\"$BAM\" INTERLEAVE=true INCLUDE_NON_PF_READS=true FASTQ=/dev/stdout \\\n | /opt/flexbar/flexbar --adapters \"$TRIMMING_ADAPTERS\" --reads - --interleaved --adapter-trim-end LTAIL --adapter-min-overlap \"$TRIMMING_ADAPTER_MIN_OVERLAP\" --adapter-error-rate 0.1 --max-uncalled 300 --stdout-reads \\\n | /usr/local/bin/bwa mem -K 100000000 -t \"$NTHREADS\" -Y -p -R \"$READGROUP\" \"$REFERENCE\" /dev/stdin | /usr/local/bin/samblaster -a --addMateTags | /opt/samtools/bin/samtools view -b -S /dev/stdin\n fi\nfi\n" ; cwl:entryname "sequence_alignment_helper.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 20000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/alignment_helper-cwl:1.1.0" ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types , ] ; cwl:stdout "refAlign.bam" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).InsertSizeMetrics.txt" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).sam" ] ; sld:type cwl:File . cwl:default false . cwl:inputBinding [ CommandLineBinding:prefix "-b" ] ; sld:type cwl:File , sld:null . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "BAIT_INTERVALS=" ] ; sld:type cwl:File . cwl:source . sld:type [ sld:items ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "R=" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type xsd:string , cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "collect HS metrics" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.bam.nameroot).$(inputs.output_prefix)-HsMetrics.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx48g" "-jar" "/usr/picard/picard.jar" "CollectHsMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; 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:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 52000 ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in , , ; cwl:out ; cwl:run . cwl:valueFrom "ALL_READS" . cwl:inputBinding [ CommandLineBinding:prefix "-1" ] ; sld:type cwl:File , sld:null . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).NameSorted.bam" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Mark duplicates and Sort" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position 4 ; cwl:valueFrom "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ) ; cwl:baseCommand ( "/bin/bash" "markduplicates_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; 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:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mark_duplicates-cwl:1.0.1" ] ; 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 $3 /dev/stdin\nfi\n" ; cwl:entryname "markduplicates_helper.sh" ] ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "cgpBigWig Converting BAM to BigWig" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(inputs.bam.nameroot).bw" ] ) ; cwl:baseCommand ( "bam2bw" "-a" "-F" "1024" ) ; 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 "quay.io/biocontainers/cgpbigwig:1.4.0--h93d22ca_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 32000 ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; cwl:inputBinding [ CommandLineBinding:prefix "TARGET_INTERVALS=" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('bam')? self.sequence.bam : null)" . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).AlignmentSummaryMetrics.txt" ] ; sld:type cwl:File . sld:fields , ; sld:type sld:record . cwl:source . a cwl:CommandLineTool ; rdfs:label "collect gc bias metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "O=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).GcBiasMetrics.txt" ] "CHART=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).GcBiasMetricsChart.pdf" ] "S=" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.sample_name).GcBiasMetricsSummary.txt" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/usr/picard/picard.jar" "CollectGcBiasMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/picard:2.23.6" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 18000 ] . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('fastq1')? self.sequence.fastq1 : null)" . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).WgsMetrics.txt" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:default true . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; sld:type cwl:File . sld:type , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "-g" ] ; sld:type xsd:string . cwl:source . a cwl:CommandLineTool ; rdfs:label "samtools flagstat" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/local/bin/samtools" "flagstat" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.11--h6270b1f_0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.bam.basename).flagstat" . cwl:source . a cwl:CommandLineTool ; rdfs:label "Creating the homer tag directory" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/bin/bash" "homer_tag_directory.sh" ) ; 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 32000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\nname=\"homer_tag_directory\"\nbam=$1\nmkdir -p $name\necho \"creating tagDir\"\n/opt/homer/bin/makeTagDirectory $name $bam\n" ; cwl:entryname "homer_tag_directory.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/homer:4.10" ] . rdfs:comment "bwa-indexed reference file" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "-r" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).bw" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_name).GcBiasMetricsSummary.txt" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "I=" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default true . cwl:in , , ; cwl:out , , ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-2" ] ; sld:type cwl:File , sld:null . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . 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:source . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:default "final" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . sld:type xsd:string . cwl:source . sld:type , . sld:type [ sld:items ; sld:type sld:array ] . sld:type xsd:int , sld:null . cwl:source ; cwl:valueFrom "$(self.file)" . cwl:source ; cwl:valueFrom "summary-$(self.label)" . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self.sequence.hasOwnProperty('fastq2')? self.sequence.fastq2 : null)" . sld:type xsd:string .