@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:inputBinding [ CommandLineBinding:position 24 ; CommandLineBinding:prefix "--sjdbGTFfile" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "trimmed_read_1.fastq" ] ; sld:type cwl:File . cwl:default -1 , 5 ; cwl:inputBinding [ CommandLineBinding:itemSeparator " " ; CommandLineBinding:position 13 ; CommandLineBinding:prefix "--alignSJstitchMismatchNmax" ; CommandLineBinding:shellQuote false ] ; sld:type [ sld:items xsd:int ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:prefix "--reads_2" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Mark duplicates and Sort" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position 4 ; cwl:valueFrom "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ) ; cwl:baseCommand ( "/bin/bash" "markduplicates_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\ndeclare MD_BARCODE_TAG\nif [ ! -z \"$6\" ]; then\n MD_BARCODE_TAG=\"BARCODE_TAG=$6\"\n/usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT \"$MD_BARCODE_TAG\" | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nelse\n /usr/bin/java -Xmx16g -jar /opt/picard/picard.jar MarkDuplicates I=$1 O=/dev/stdout ASSUME_SORT_ORDER=$5 METRICS_FILE=$4 QUIET=true COMPRESSION_LEVEL=0 VALIDATION_STRINGENCY=LENIENT | /usr/bin/sambamba sort -t $2 -m 18G -o $3 /dev/stdin\nfi\n" ; cwl:entryname "markduplicates_helper.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 40000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mark_duplicates-cwl:1.0.1" ] . cwl:source . cwl:in , ; cwl:out , ; cwl:run . cwl:in , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:in , , , , ; cwl:out , , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "trimmed_read_*.fastq" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:default "/usr/local/bin/STAR" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--STAR_PATH" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--max-uncalled" ] ; sld:type xsd:int . a cwl:CommandLineTool ; rdfs:label "STAR-Fusion identify candidate fusion transcript" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--CPU" "$(runtime.cores)" ) ; cwl:baseCommand ( "/usr/local/src/STAR-Fusion/STAR-Fusion" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "trinityctat/starfusion:1.8.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 10 ; ResourceRequirement:ramMin 64000 ] . sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:default 10 ; cwl:inputBinding [ CommandLineBinding:position 18 ; CommandLineBinding:prefix "--chimNonchimScoreDropMin" ] ; sld:type xsd:int . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.reads1.nameroot).strandness_check.txt" ] ; sld:type cwl:File . sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "kallisto/abundance.tsv" ] ; sld:type cwl:File . sld:type xsd:int . cwl:in , , , ; cwl:out , ; cwl:run . cwl:source . a cwl:CommandLineTool ; rdfs:label "samtools index" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.bam.basename)" "$(runtime.outdir)/$(inputs.bam.basename).bai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "cp" "$(inputs.bam.basename).bai" "$(runtime.outdir)/$(inputs.bam.nameroot).bai" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "${ var f = inputs.bam; delete f.secondaryFiles; return f }" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] . sld:type cwl:File . cwl:default "12" ; cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--chimJunctionOverhangMin" ] ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "read1.fastq" ] ; sld:type cwl:File . sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "rna_metrics.txt" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile_name_prefix)Aligned.out.bam" ] ; sld:type cwl:File . cwl:source . cwl:default 10 ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "--alignSJDBoverhangMin" ] ; sld:type xsd:int . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "--kallisto_index" ] ; sld:type cwl:File . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "trimmed_read_2.fastq" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "kallisto/abundance.h5" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "I=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . sld:type cwl:File . cwl:in ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if (inputs.strand) {\n if (inputs.strand == 'first') {\n return ['--rf'];\n } else if (inputs.strand == 'second') {\n return ['--fr'];\n } else {\n return [];\n }\n } else {\n return []\n }\n}\n" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:default "BAM" , "Unsorted" ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--outSAMtype" ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if (inputs.strand) {\n if (inputs.strand == 'first') {\n return ['--rf-stranded'];\n } else if (inputs.strand == 'second') {\n return ['--fr-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:default 1 ; cwl:inputBinding [ CommandLineBinding:position 21 ; CommandLineBinding:prefix "--chimOutJunctionFormat" ] ; sld:type xsd:int . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:source . 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" "$(runtime.cores)" "-e" ) ; cwl:baseCommand ( "/usr/bin/stringtie" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 12 ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/rnaseq:1.0.0" ] . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; 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:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bisulfite:v1.4" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 16000 ; ResourceRequirement:tmpdirMin 25000 ] . sld:type cwl:Directory . cwl:in , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile_name_prefix)Log.out" ] ; sld:type cwl:File . cwl:default "alignReads" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--runMode" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-l" ] ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ sld:items [ sld:items cwl:File ; sld:type sld:array ] ; sld:type sld:array ] . cwl:default "Basic" ; cwl:inputBinding [ CommandLineBinding:position 23 ; CommandLineBinding:prefix "--twopassMode" ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "read2.fastq" ] ; sld:type cwl:File . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , , , , , , ; cwl:out , , ; cwl:run . a cwl:CommandLineTool ; rdfs:label "STAR: align reads to transcriptome" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--runThreadN" "$(runtime.cores)" ) ; cwl:baseCommand ( "/usr/local/bin/STAR" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 10 ; ResourceRequirement:ramMin 64000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/star:2.7.0f" ] . cwl:outputBinding [ CommandOutputBinding:glob "gene_abundance.tsv" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type cwl:File . 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:1.0.0" ] . cwl:source . cwl:default "12" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--chimSegmentMin" ] ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--adapter-min-overlap" ] ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile_name_prefix)Log.progress.out" ] ; sld:type cwl:File . cwl:source . cwl:default 100000 ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--alignMatesGapMax" ] ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "RIBOSOMAL_INTERVALS=" ; CommandLineBinding:separate false ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).mark_dups_metrics.txt" ] ; sld:type cwl:File . cwl:default 1e-01 ; cwl:inputBinding [ CommandLineBinding:position 20 ; CommandLineBinding:prefix "--peOverlapMMp" ] ; sld:type xsd:float . cwl:source . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 5 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position 4 ; CommandLineBinding:prefix "--readFilesIn" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type cwl:File . cwl:source . sld:type cwl:Directory . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "I=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:default "coordinate" . cwl:source . cwl:default "STAR-Fusion_outdir" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--output_dir" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:inputBinding [ cwl:valueFrom "${\n if (inputs.strand) {\n if (inputs.strand == 'first') { \n return ['STRAND=SECOND_READ_TRANSCRIPTION_STRAND'];\n } else if (inputs.strand == 'second') {\n return ['STRAND=FIRST_READ_TRANSCRIPTION_STRAND'];\n } else {\n return ['STRAND=NONE'];\n }\n } else {\n return ['STRAND=NONE']\n }\n}\n" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:inputBinding [ CommandLineBinding:prefix "--gtf" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--reads" ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:int . sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--adapter-trim-end" ] ; sld:type xsd:string . cwl:default "Within" ; cwl:inputBinding [ CommandLineBinding:position 15 ; CommandLineBinding:prefix "--outSAMunmapped" ] ; sld:type xsd:string . cwl:in , ; cwl:out ; cwl:run . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "sorted.bam" ; sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:default 100000 ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "--alignIntronMax" ] ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fusion_output_dir +\"/star-fusion.fusion_predictions.abridged.tsv\")" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:comment "Uses how_are_we_stranded_here, a python package for testing strandedness. Runs Kallisto and Rseqc (infer-experiment-py) to\nto check which direction reads align once mapped in transcripts. It first creates a Kallisto index (or uses a pre-made index)\nof your organism's transcriptome. It then maps a small subset of reads (default 200000) to the transcriptome and uses Kallisto's\n--genomebam argument to project pseudoalignments to the genome sorted BAM file. (Currently only Kallisto version 0.44.0 works well with\nhow_are_we_stranded_here.) It finally runs RSeQC's infer_experiment.py to check which direction reads from the first and second pairs\nare aligned in relation to the transcript strand, and provides output with the likely strandedness of your data.\n" ; rdfs:label "runs how_are_we_stranded_here to determine RNAseq data strandedness" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--print_commands" ) ; cwl:baseCommand ( "check_strandedness" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ; ResourceRequirement:tmpdirMin 5000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "smk5g5/checkstranded:version1.0" ] ; cwl:stdout "$(inputs.reads1.nameroot).strandness_check.txt" . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "NH" , "HI" , "AS" , "MD" , "NM" ; cwl:inputBinding [ CommandLineBinding:itemSeparator " " ; CommandLineBinding:position 27 ; CommandLineBinding:prefix "--outSAMattributes" ; CommandLineBinding:shellQuote false ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile_name_prefix)Log.final.out" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-J" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile_name_prefix)SJ.out.tab" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.outfile_name_prefix)Chimeric.out.junction" ] ; 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:1.0.0" ] . rdfs:comment " fusion genome dir directory containing genome lib (see http://STAR-Fusion.github.io) " ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--genome_lib_dir" ] ; sld:type cwl:Directory . cwl:inputBinding [ CommandLineBinding:position 50 ] ; sld:type cwl:File . sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "bam to trimmed fastqs" ; 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:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "kallisto/fusion.txt" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . rdfs:comment " specifies path to the directory where the genome indices are stored " ; cwl:inputBinding [ CommandLineBinding:position 22 ; CommandLineBinding:prefix "--genomeDir" ] ; sld:type cwl:Directory . cwl:default "intronMotif" ; cwl:inputBinding [ CommandLineBinding:position 14 ; CommandLineBinding:prefix "--outSAMstrandField" ] ; sld:type xsd:string . 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=$(runtime.outdir)/rna_metrics.pdf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx16g" "-jar" "/opt/picard/picard.jar" "CollectRnaSeqMetrics" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/rnaseq:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 18000 ] . cwl:default 12 ; cwl:inputBinding [ CommandLineBinding:position 19 ; CommandLineBinding:prefix "--peOverlapNbasesMin" ] ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--reads2" ] ; sld:type cwl:File . cwl:source . cwl:default "cat" ; cwl:inputBinding [ CommandLineBinding:position 26 ; CommandLineBinding:prefix "--readFilesCommand" ] ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . a cwl:CommandLineTool ; rdfs:label "samtools sort" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:prefix "-o" ; cwl:valueFrom "$(runtime.outdir)/$(inputs.output_filename)" ] [ CommandLineBinding:prefix "-@" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "sort" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] . cwl:default "queryname" ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:string . cwl:in , , ; cwl:out , , ; cwl:run . 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 ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs , , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 8 ; ResourceRequirement:ramMin 32000 ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/rnaseq:1.0.0" ] . cwl:in , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:default "MarkedSorted.bam" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type xsd:string , sld:null . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--min-read-length" ] ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:prefix "--reads_1" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , ; cwl:out , , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--adapters" ] ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:prefix "--transcripts" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "rna_metrics.pdf" ] ; sld:type cwl:File , sld:null . sld:type [ sld:items xsd:string ; sld:type sld:array ] . rdfs:comment " string(s): SAM/BAM read group line. The first word contains the read group identifier and must start with ID:, e.g. –outSAMattrRGline ID:xxx CN:yy DS:z z z. xxx will be added as RG tag to each output alignment. Any spaces in the tag values have to be double quoted. Comma separated RG lines correspons to different (comma separated) input files in –readFilesIn " ; cwl:inputBinding [ CommandLineBinding:itemSeparator " , " ; CommandLineBinding:position 16 ; CommandLineBinding:prefix "--outSAMattrRGline" ; CommandLineBinding:shellQuote false ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . sld:type xsd:int . sld:type xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:default 3 ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "--chimSegmentReadGapMax" ] ; sld:type xsd:int . cwl:default 10 ; cwl:inputBinding [ CommandLineBinding:position 17 ; CommandLineBinding:prefix "--chimMultimapNmax" ] ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "stringtie_transcripts.gtf" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "stringtie_gene_expression.tsv" ] ; sld:type cwl:File . sld:type xsd:int . cwl:linkMerge "merge_flattened" ; cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-G" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.fusion_output_dir +\"/star-fusion.fusion_predictions.tsv\")" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_filename)" ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "STAR-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:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:prefix "REF_FLAT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . sld:type cwl:File . cwl:default "STAR_" ; cwl:inputBinding [ CommandLineBinding:position 25 ; CommandLineBinding:prefix "--outFileNamePrefix" ] ; sld:type xsd:string . cwl:source . cwl:default "None" ; cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--outReadsUnmapped" ] ; sld:type xsd:string .