class: Workflow cwlVersion: v1.0 $namespaces: edam: 'http://edamontology.org/' s: 'http://schema.org/' label: Identifies non-coding RNAs using Rfams covariance models inputs: clan_info: type: File cores: type: int covariance_models: type: File[] query_sequences: type: File catOutputFileName: type: string default: full_cmsearch_output outputs: deoverlapped_matches: outputSource: remove_overlaps/deoverlapped_matches type: File steps: cmsearch: label: Search sequence(s) against a covariance model database run: ../tools/Infernal/cmsearch/infernal-cmsearch-v1.1.2.cwl scatter: covariance_model_database in: covariance_model_database: covariance_models cpu: cores omit_alignment_section: default: true only_hmm: default: true query_sequences: query_sequences search_space_size: default: 1000 out: [ matches, programOutput ] concatenate_matches: run: ../utils/concatenate.cwl in: files: cmsearch/matches outputFileName: catOutputFileName out: - result remove_overlaps: label: Remove lower scoring overlaps from cmsearch --tblout files. run: ../tools/cmsearch-deoverlap/cmsearch-deoverlap-v0.02.cwl in: clan_information: clan_info cmsearch_matches: concatenate_matches/result out: - deoverlapped_matches requirements: - class: ScatterFeatureRequirement $schemas: - 'http://edamontology.org/EDAM_1.16.owl' - 'https://schema.org/docs/schema_org_rdfa.html' 's:copyrightHolder': EMBL - European Bioinformatics Institute 's:license': 'https://www.apache.org/licenses/LICENSE-2.0' 's:author': Maxim Scheremetjew