class: Workflow cwlVersion: v1.0 dct:creator: {'@id': 'http://orcid.org/0000-0002-7681-6415', 'foaf:mbox': genomehacker@synapse.org, 'foaf:name': genomehacker} doc: 'SMC-RNA challenge fusion detection submission GSTRUCT-fusion workflow: tar genome index, align with GSNAP, analyze with GSTRUCT-fusion' hints: [] id: main inputs: - {id: TUMOR_FASTQ_1, type: File} - {id: TUMOR_FASTQ_2, type: File} - {id: index, type: File} name: main outputs: - {id: OUTPUT, outputSource: gstruct-fusion/output, type: File} steps: - id: gsnap in: - {id: dbdir, source: tar/output} - {id: fastq1, source: TUMOR_FASTQ_1} - {id: fastq2, source: TUMOR_FASTQ_2} - {default: sam, id: format} - {default: GRCh37.75, id: gmapdb} - {default: true, id: gunzip} - {default: true, id: nosamheaders} - {default: 5, id: noutputs} - {default: 1, id: novelsplicing} - {default: 4, id: nthreads} - {default: ensembl.known.splicesites, id: splicingfile} out: [output] run: gsnap.cwl - id: gstruct-fusion in: - {id: aligndir, source: gsnap/output} - {id: dbdir, source: tar/output} - {default: ensembl.known.genes, id: genesfile} - {default: GRCh37.75, id: gmapdb} - {default: sample, id: samplename} out: [output] run: gstruct-fusion.cwl - id: tar in: - {id: input, source: index} out: [output] run: tar.cwl