#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow inputs: table_hits: type: File label: output of infernal's cmscan or cmsearch outputs: SSU_coordinates: type: File outputSource: extract_coords/matched_seqs_with_coords steps: grep: run: pull-SSUs.cwl in: { hits: table_hits } out: [ SSUs ] extract_coords: run: extract-coords-from-cmscan.cwl in: { infernal_matches: grep/SSUs } out: [ matched_seqs_with_coords ] $namespaces: s: http://schema.org/ $schemas: - https://schema.org/docs/schema_org_rdfa.html s:license: "https://www.apache.org/licenses/LICENSE-2.0" s:copyrightHolder: "EMBL - European Bioinformatics Institute"