build_workflow.py

from cwlgen.import_cwl import parse_cwl
from cwlgen import File, Workflow
from cwlgen.workflow import InputParameter

# Files in https://github.com/Duke-GCB/bespin-cwl/tree/qiime2-workflow

mkdir_tool = parse_cwl('EMPSingleEndSequences-directory.cwl')
import_tool = parse_cwl('tools-import.cwl')

w = Workflow()

# Add steps
step1 = w.add('make_import_directory', mkdir_tool, {
    'sequences': File(''), # File is a stub, but requires an unused 'path' parameter
    'barcodes': File(''),
})
step2 = w.add('make_sequences_artifact', import_tool, {
    'input_path': step1['dir'], 
    'type': InputParameter('sequences_artifact_type', param_type='string'),
})
step2['sequences_artifact'].store()
w.label = 'qiime2 importing data'
w.doc = 'Obtaining and importing data from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/'

w.export()

output.cwl

#!/usr/bin/env cwl-runner

class: Workflow
cwlVersion: v1.0
doc: Obtaining and importing data from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/
inputs:
  barcodes: {id: barcodes, type: File}
  sequences: {id: sequences, type: File}
  sequences_artifact_type: {id: sequences_artifact_type, type: string}
label: qiime2 importing data
outputs:
  make_sequences_artifact_sequences_artifact: {id: make_sequences_artifact_sequences_artifact,
    outputSource: make_sequences_artifact/sequences_artifact, type: File}
steps:
  make_import_directory:
    id: make_import_directory
    in: {barcodes: barcodes, sequences: sequences}
    out: [dir]
    run: EMPSingleEndSequences-directory.cwl
  make_sequences_artifact:
    id: make_sequences_artifact
    in: {input_path: make_import_directory/dir, sequences_artifact_type: sequences_artifact_type}
    out: [sequences_artifact]
    run: tools-import.cwl