cwlVersion: v1.0 class: Workflow label: Find reads with predicted coding sequences above 60 AA in length requirements: ScatterFeatureRequirement: {} SchemaDefRequirement: types: - $import: ../tools/FragGeneScan-model.yaml inputs: sequence: type: File format: edam:format_1929 # FASTA completeSeq: boolean model: ../tools/FragGeneScan-model.yaml#model outputs: predicted_CDS_aa: type: File format: edam:format_1929 # FASTA outputSource: combine_predicted_CDS_aa/result predicted_CDS_nuc: type: File format: edam:format_1929 # FASTA outputSource: combine_predicted_CDS_nuc/result steps: split_seqs: run: ../tools/fasta_chunker.cwl in: seqs: sequence chunk_size: { default: 100000 } out: [ chunks ] ORF_prediction: doc: | Find reads with predicted coding sequences (pCDS) run: ../tools/FragGeneScan1_20.cwl in: sequence: split_seqs/chunks completeSeq: completeSeq model: model scatter: sequence out: [ predicted_CDS_aa, predicted_CDS_nuc ] combine_predicted_CDS_aa: run: ../tools/concatenate.cwl in: files: ORF_prediction/predicted_CDS_aa out: [ result ] combine_predicted_CDS_nuc: run: ../tools/concatenate.cwl in: files: ORF_prediction/predicted_CDS_nuc out: [ result ] $namespaces: edam: http://edamontology.org/ s: http://schema.org/ $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"