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