#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.0 inputs: proteins_to_align: type: File label: proteins nucleotides: File outputs: alignment1: type: File outputSource: clustal/alignment label: proteins alignment guide_tree: type: File outputSource: clustal/guide_tree label: guide tree alignment2: type: File outputSource: pal2nal/alignment label: nucleotides alignment results: type: File outputSource: codeml/results label: dN/dS results steps: clustal: run: clustalo.cwl in: multi_sequence: proteins_to_align out: [alignment, guide_tree] pal2nal: run: pal2nal.cwl in: protein_alignment: clustal/alignment nucleotides: nucleotides out: [alignment] codeml: run: codeml.cwl in: sequences: pal2nal/alignment tree: clustal/guide_tree out: [results]