#!/usr/bin/env cwl-runner
class: Workflow

cwlVersion: v1.0

inputs:
    proteins_to_align: File
    nucleotides: File

outputs:
    alignment1: { type: File, outputSource: clustal/alignment }
    guide_tree: { type: File, outputSource: clustal/guide_tree }
    alignment2: { type: File, outputSource: pal2nal/alignment }
    results: { type: File, outputSource: codeml/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:
       seq: pal2nal/alignment
       tree: clustal/guide_tree
    out: [results]