womtool fails on python code in task's command when "_" used as a variable in a list comprehension

myourshawmyourshaw University of ColoradoMember

In a task's command block that has a python <<CODE block, womtool gets this error:

Unrecognized token on line 356, column 43:

        barcode_data.append([barcode_dict[_] for _ in header])

Replacing the underscore with 'x' resolves the problem.

The full task:

task CreateBarcodeFile {
  String python3_cmd
  File run_metadata
  Int lane

  command {
    ${python3_cmd} <<CODE
    barcode_data = []

    with open('${run_metadata}', 'r') as ifh:
        metadata = json.load(ifh)

    if metadata['NUM_INDICES'] == 1:
        header = ['barcode_sequence_1', 'barcode_name', 'library_name']
        header = ['barcode_sequence_1', 'barcode_sequence_2', 'barcode_name', 'library_name']

    lane_metadata = metadata['LANE_METADATA'].get(str(lane))
    for sample_metadata in lane_metadata:
        barcode_1 = sample_metadata['BARCODE_1']
        barcode_2 = sample_metadata.get('BARCODE_2', '')

        barcode_dict = {
            'barcode_sequence_1': barcode_1,
            'barcode_sequence_2': barcode_2,
            'barcode_name': sample_metadata['BARCODE_NAME'],
            'library_name': sample_metadata['LIBRARY_NAME'],
        barcode_data.append([barcode_dict[_] for _ in header])


    for d in barcode_data:
  runtime {
    memory: "1G"
    cpu: 1
  output {
    File barcode_file = stdout()

Best Answers


  • myourshawmyourshaw University of ColoradoMember

    Thanks Chris! Using <<< >>> also fixed the next problem I was having. And nice catch on the lane variable, an annoying problem when copying from PyCharm into a wdl.

    I had been using Sublime Text for wdl files, which about a year ago had a slightly better wdl plugin than PyCharm, but was not smart enough to detect how wdl is fooled by the braces. I'll be switching to the PyCharm one now. Thanks for the tip.

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