cwlVersion: v1.0 class: Workflow label: analysis for assembled sequences doc: rna / protein - qc, annotation, index, abundance requirements: - class: StepInputExpressionRequirement - class: InlineJavascriptRequirement - class: ScatterFeatureRequirement - class: MultipleInputFeatureRequirement - class: SubworkflowFeatureRequirement inputs: jobid: string sequences: File # static DBs m5nrBDB: File m5nrFull: File[] m5nrSCG: File m5rnaFull: File m5rnaClust: File m5rnaIndex: Directory m5rnaPrefix: string outputs: assemblyCoverage: type: File outputSource: qcAssemble/assemblyCoverage seqStatOut: type: File outputSource: qcAssemble/seqStatFile seqBinOut: type: File outputSource: qcAssemble/seqBinFile qcStatOut: type: File outputSource: qcAssemble/qcStatFile qcSummaryOut: type: File outputSource: qcAssemble/qcSummaryFile rnaFeatureOut: type: File outputSource: rnaAnnotate/rnaFeatureOut rnaClustSeqOut: type: File outputSource: rnaAnnotate/rnaClustSeqOut rnaClustMapOut: type: File outputSource: rnaAnnotate/rnaClustMapOut rnaSimsOut: type: File outputSource: rnaAnnotate/rnaSimsOut protFeatureOut: type: File outputSource: protAnnotate/protFeatureOut protFilterFeatureOut: type: File outputSource: protAnnotate/protFilterFeatureOut protClustSeqOut: type: File outputSource: protAnnotate/protClustSeqOut protClustMapOut: type: File outputSource: protAnnotate/protClustMapOut protSimsOut: type: File outputSource: protAnnotate/protSimsOut simSeqOut: type: File outputSource: indexSimSeq/simSeqOut md5ProfileOut: type: File outputSource: abundance/md5ProfileOut lcaProfileOut: type: File outputSource: abundance/lcaProfileOut sourceStatsOut: type: File outputSource: abundance/sourceStatsOut darkmatterOut: type: File outputSource: darkmatter/output steps: qcAssemble: run: ../Workflows/qc-assembled.workflow.cwl in: jobid: jobid sequences: sequences kmerLength: valueFrom: ${ return [6, 15]; } out: [assemblyCoverage, seqStatFile, seqBinFile, qcStatFile, qcSummaryFile] rnaAnnotate: run: ../Workflows/rna-annotation.workflow.cwl in: jobid: jobid sequences: sequences m5nrBDB: m5nrBDB m5rnaFull: m5rnaFull m5rnaClust: m5rnaClust m5rnaIndex: m5rnaIndex m5rnaPrefix: m5rnaPrefix out: [rnaFeatureOut, rnaClustSeqOut, rnaClustMapOut, rnaSimsOut, rnaFilterOut, rnaExpandOut, rnaLCAOut] protAnnotate: run: ../Workflows/protein-filter-annotation.workflow.cwl in: jobid: jobid sequences: sequences rnaSims: rnaAnnotate/rnaSimsOut rnaClustMap: rnaAnnotate/rnaClustMapOut m5nrBDB: m5nrBDB m5nrFull: m5nrFull m5nrSCG: m5nrSCG out: [protFeatureOut, protFilterFeatureOut, protClustSeqOut, protClustMapOut, protSimsOut, protFilterOut, protExpandOut, protLCAOut] indexSimSeq: run: ../Workflows/index_sim_seq.workflow.cwl in: jobid: jobid featureSeqs: source: - rnaAnnotate/rnaFeatureOut - protAnnotate/protFeatureOut filterSims: source: - rnaAnnotate/rnaFilterOut - protAnnotate/protFilterOut clustMaps: source: - rnaAnnotate/rnaClustMapOut - protAnnotate/protClustMapOut out: [simSeqOut, indexOut] abundance: run: ../Workflows/abundance-clca.workflow.cwl in: jobid: jobid md5index: indexSimSeq/indexOut coverage: qcAssemble/assemblyCoverage filterSims: source: - rnaAnnotate/rnaFilterOut - protAnnotate/protFilterOut expandSims: source: - rnaAnnotate/rnaExpandOut - protAnnotate/protExpandOut rnaExpandLca: rnaAnnotate/rnaLCAOut protExpandLca: protAnnotate/protLCAOut rnaClustMap: rnaAnnotate/rnaClustMapOut protClustMap: protAnnotate/protClustMapOut m5nrSCG: m5nrSCG out: [md5ProfileOut, lcaProfileOut, sourceStatsOut] darkmatter: run: ../Tools/extract_darkmatter.tool.cwl in: geneSeq: protAnnotate/protFilterFeatureOut simHit: source: - rnaAnnotate/rnaSimsOut - protAnnotate/protSimsOut clustMap: source: - rnaAnnotate/rnaClustMapOut - protAnnotate/protClustMapOut outName: source: jobid valueFrom: $(self).750.darkmatter.faa out: [output]