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miniwdl run doesn't understand interleaved positional & optional/flag args

Open mlin opened this issue 3 years ago • 0 comments

When you miniwdl run myworkflow.wdl input1=value1 input2.value2, you can't interleave flags (such as --verbose or --dir) in the sequence myworkflow.wdl input1=value1 input2.value2 which have to be contiguous. This seems to be a longstanding property of python argparse discussed here: https://bugs.python.org/issue14191

That issue led to the addition of argparse.parse_intermixed_args() in Python 3.7. But that's newer than we claim to support, and the docs state it doesn't work with subparsers (which we use).

mlin avatar Mar 19 '21 18:03 mlin