class: Workflow cwlVersion: v1.0 label: >- TransDecoder 2 step workflow, running TransDecoder.LongOrfs (step 1) followed by TransDecoder.Predict (step2) $namespaces: edam: 'http://edamontology.org/' s: 'http://schema.org/' inputs: singleBestOnly: type: boolean? transcriptsFile: format: edam:format_1929 # FASTA type: File outputs: bed_output: outputSource: predict_coding_regions/bed_output type: File coding_regions: outputSource: predict_coding_regions/coding_regions type: File gff3_output: outputSource: predict_coding_regions/gff3_output type: File peptide_sequences: outputSource: predict_coding_regions/peptide_sequences type: File steps: extract_long_orfs: label: Extracts the long open reading frames run: ../tools/TransDecoder/TransDecoder.LongOrfs-v5.cwl in: transcriptsFile: transcriptsFile out: - workingDir predict_coding_regions: label: Predicts the likely coding regions run: ../tools/TransDecoder/TransDecoder.Predict-v5.cwl in: longOpenReadingFrames: extract_long_orfs/workingDir singleBestOnly: singleBestOnly transcriptsFile: transcriptsFile out: - bed_output - coding_regions - gff3_output - peptide_sequences $schemas: - 'http://edamontology.org/EDAM_1.16.owl' - 'https://schema.org/docs/schema_org_rdfa.html' s:license: "https://www.apache.org/licenses/LICENSE-2.0" s:copyrightHolder: "EMBL - European Bioinformatics Institute, 2018" s:author: "Maxim Scheremetjew"