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Check return code of every subprocess command #19

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martinghunt opened this issue Nov 22, 2021 · 3 comments
Open

Check return code of every subprocess command #19

martinghunt opened this issue Nov 22, 2021 · 3 comments

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@martinghunt
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and handle it. eg currently assembly can work but make VCF can fail. We don't find out because the whole thing crashes. Fixing this should cover #5 as well.
@iqbal-lab
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not sure if this is open @martinghunt

@martinghunt martinghunt mentioned this issue Dec 16, 2021
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@martinghunt
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it is open

@bede
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bede commented Dec 16, 2021

subprocess.run() can take check=True
https://github.com/iqbal-lab-org/viridian_workflow/blob/9ec3d8035c8d8df50a8ccaa2b7ca17946164ff8d/viridian_workflow/utils.py#L49

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@bede @martinghunt @iqbal-lab