@prefix LoadListingRequirement: . @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:outputBinding [ CommandOutputBinding:glob "trimmed_read_1.fastq" ] ; sld:type cwl:File . cwl:in , , ; cwl:out , , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "trimmed_read_*.fastq" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if (inputs.strand) {\n if (inputs.strand == 'first') {\n return ['--rf'];\n } else if (inputs.strand == 'second') {\n return ['--fr'];\n } else {\n return [];\n }\n } else {\n return []\n }\n}\n" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , ; cwl:out ; cwl:run . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "samtools index" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.bam.basename)" "$(runtime.outdir)/$(inputs.bam.basename).bai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.bam.basename).bai" "$(runtime.outdir)/$(inputs.bam.nameroot).bai" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.bam; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--rg" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -2 ; CommandLineBinding:prefix "-1" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Picard: RNA Seq Metrics" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "O=$(runtime.outdir)/rna_metrics.txt" ] [ cwl:valueFrom "CHART=$(runtime.outdir)/rna_metrics.pdf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/picard/picard.jar" "CollectRnaSeqMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/rnaseq" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 18000 ] . cwl:source ; cwl:valueFrom "$(self[0])" . cwl:in ; cwl:out , ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if (inputs.strand) {\n if (inputs.strand == 'first') {\n return ['--fr-stranded'];\n } else if (inputs.strand == 'second') {\n return ['--rf-stranded'];\n } else {\n return [];\n }\n } else {\n return [];\n }\n}\n" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:outputBinding [ CommandOutputBinding:glob "trimmed_read_2.fastq" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--adapters" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "StringTie" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" "$(runtime.outdir)/stringtie_transcripts.gtf" "-A" "$(runtime.outdir)/stringtie_gene_expression.tsv" "-p" "$(runtime.cores)" "-e" ) ; cwl:baseCommand ( "/usr/bin/stringtie" ) ; 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/rnaseq" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 12 ; ResourceRequirement:ramMin 16000 ] . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "RIBOSOMAL_INTERVALS=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:in , ; cwl:out , ; cwl:run . cwl:in , , , , , , ; cwl:out ; cwl:run . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--adapter-trim-end" ] ; sld:type xsd:string . cwl:source . sld:type cwl:File . sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "kallisto/fusion.txt" ] ; sld:type cwl:File . sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position -1 ; CommandLineBinding:prefix "-2" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "REF_FLAT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source ; cwl:valueFrom "$(self[1])" . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Kallisto: TranscriptToGene" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/src/transcript_to_gene.R" ) ; cwl:baseCommand ( "/usr/local/bin/Rscript" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 2000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/rnaseq" ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type cwl:File . cwl:default "MarkedSorted.bam" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string , sld:null . sld:type [ sld:items [ sld:items xsd:string ; sld:type sld:array ] ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "kallisto/abundance.h5" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Trim FASTQ (flexbar)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--target" [ cwl:valueFrom "$(runtime.outdir)/trimmed_read" ] "--threads" [ cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/opt/flexbar/flexbar" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 16000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bisulfite:v1.4" ] . rdfs:comment "the species being analyzed, such as homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Kallisto: Quant" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "quant" "-t" "$(runtime.cores)" "-b" "100" "--fusion" "-o" "kallisto" ) ; cwl:baseCommand ( "/usr/bin/kallisto" ) ; 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 8 ; ResourceRequirement:ramMin 32000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/rnaseq" ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "I=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "stringtie_gene_expression.tsv" ] ; sld:type cwl:File . cwl:in , , , , , , , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--max-uncalled" ] ; sld:type xsd:int . cwl:source . sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "stringtie_transcripts.gtf" ] ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--min-read-length" ] ; sld:type xsd:int . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ cwl:valueFrom "${\n if (inputs.strand) {\n if (inputs.strand == 'first') { \n return ['STRAND=SECOND_READ_TRANSCRIPTION_STRAND'];\n } else if (inputs.strand == 'second') {\n return ['STRAND=FIRST_READ_TRANSCRIPTION_STRAND'];\n } else {\n return ['STRAND=NONE'];\n }\n } else {\n return ['STRAND=NONE']\n }\n}\n" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:outputBinding [ CommandOutputBinding:glob "rna_metrics.pdf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ sld:items [ sld:items cwl:File ; sld:type sld:array ] ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "read1.fastq" ] ; sld:type cwl:File . sld:type xsd:int . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "rna_metrics.txt" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "I=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . sld:type cwl:File . cwl:in , , , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "aligned.bam" ] ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--adapter-min-overlap" ] ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "gene_abundance.tsv" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Mark duplicates and Sort" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(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: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:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 40000 ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--reads" ] ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position -5 ; CommandLineBinding:prefix "--rg-id" ] ; sld:type xsd:string . a cwl:Workflow ; rdfs:label "bam to trimmed fastqs and HISAT alignments" ; 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:MultipleInputFeatureRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "kallisto/abundance.tsv" ] ; sld:type cwl:File . sld:type cwl:File . a cwl:Workflow ; rdfs:label "RNA-Seq alignment and transcript/gene abundance workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int . a cwl:CommandLineTool ; rdfs:label "HISAT2: align" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-p" "$(runtime.cores)" "--dta" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/usr/bin/sambamba" "view" "-S" "-f" "bam" "-l" "0" "/dev/stdin" [ CommandLineBinding:shellQuote false ; cwl:valueFrom "|" ] "/usr/bin/sambamba" "sort" "-t" "$(runtime.cores)" "-m" "8G" "-o" "$(runtime.outdir)/aligned.bam" "/dev/stdin" ) ; cwl:baseCommand ( "/usr/bin/hisat2" ) ; 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 16 ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/rnaseq" ] . sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "read2.fastq" ] ; sld:type cwl:File . cwl:source . sld:type xsd:int . cwl:source . sld:type xsd:string . sld:type cwl:File . cwl:default "queryname" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:string . cwl:in , , , ; cwl:out , ; cwl:run . cwl:default "coordinate" . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--reads2" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . rdfs:comment "the assembly used, such as GRCh37/38, GRCm37/38" ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-G" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "-x" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Sambamba: merge" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(runtime.cores)" "$(runtime.outdir)/merged.bam" ) ; cwl:baseCommand ( "/usr/bin/sambamba_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/biscuit:0.3.8.2" ] . a cwl:CommandLineTool ; rdfs:label "Picard: BAM to FASTQ" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "F=$(runtime.outdir)/read1.fastq" ] [ cwl:valueFrom "F2=$(runtime.outdir)/read2.fastq" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/picard/picard.jar" "SamToFastq" "VALIDATION_STRINGENCY=SILENT" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/rnaseq" ] . cwl:inputBinding [ CommandLineBinding:position -6 ; cwl:valueFrom "${\n if (inputs.strand) {\n if (inputs.strand == 'first') {\n return ['--rna-strandness RF'];\n } else if (inputs.strand == 'second') {\n return ['--rna-strandness FR'];\n } else {\n return [];\n }\n } else {\n return []\n }\n}\n" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "merged.bam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source .