checkm-subwf.cwl

#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow

requirements:
  SubworkflowFeatureRequirement: {}
  MultipleInputFeatureRequirement: {}
  InlineJavascriptRequirement: {}
  StepInputExpressionRequirement: {}
  ScatterFeatureRequirement: {}

inputs:
  genomes_folder: Directory

outputs:

  checkm_csv:
    type: File
    outputSource: checkm2csv/csv

steps:

  checkm:
    run: ../../tools/checkm/checkm.cwl
    in:
      input_folder: genomes_folder
      checkm_outfolder: { default: 'checkm_outfolder' }
    out: [ stdout, out_folder ]

  checkm2csv:
    run: ../../tools/checkm/checkm2csv.cwl
    in:
      out_checkm: checkm/stdout
    out: [ csv ]