#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: ScatterFeatureRequirement: {} inputs: hits: File[] outputs: unique_hits: type: File outputSource: sort_uniq_names/sorted_uniq_names steps: extract_coord_lines: run: extract_coord_lines.cwl in: { summary: hits } scatter: summary out: [ coord_lines ] extract_names: run: id: extract_names # TODO, remove when toil upgrade to a newer cwltool class: CommandLineTool inputs: coordinate_lines: type: File inputBinding: { position: 1 } doc: | The required columns are as follows: (1) target name: The name of the target sequence or profile. baseCommand: [ awk, '{print $1}' ] stdout: names # helps with cwltool's --cache outputs: { names: { type: stdout } } in: { coordinate_lines: extract_coord_lines/coord_lines } scatter: coordinate_lines out: [ names ] sort_uniq_names: run: id: sort_uniq_names # TODO, remove when toil upgrades to a newer cwltool class: CommandLineTool inputs: names: type: File[] inputBinding: { position: 1 } baseCommand: [ sort, --unique ] stdout: sorted_uniq_names # helps with cwltool's --cache outputs: { sorted_uniq_names: stdout } in: { names: extract_names/names } out: [ sorted_uniq_names ] $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"