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Fix configargparse parsing wrong in toil-cwl-runner #4615

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unito-bot opened this issue Oct 10, 2023 · 0 comments · Fixed by #4618
Closed

Fix configargparse parsing wrong in toil-cwl-runner #4615

unito-bot opened this issue Oct 10, 2023 · 0 comments · Fixed by #4618

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@unito-bot
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In toil-cwl-runner, configargparse sometimes doesn’t work due to a bug it has. We need a workaround for it.

If nargs=argparse.remainder on an argument, configargparse will not collect the right arguments, because the arguments from the config get tacked on the end of the argument list and can get eaten.

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1407
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Fix configargparse in CWL DataBiosphere/toil
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