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viral-ngs
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demux failures silently swallowed by dnanexus #47

Closed dpark01 closed 7 years ago

dpark01 commented 7 years ago

Looking at job-BzVxfZj0jy1P2gG479y0qb0K, it appears that failures during demux are not triggering failures in the DNAnexus job, even though I'm pretty sure our code emits a non-zero exit code.

dpark01 commented 7 years ago

(this might be true in other steps too, e.g. refine1/refine2)

yifei-men commented 7 years ago

@mlin I didn't go hunt down the job, but I believe this is a bug I introduced >.<

I disabled -e error because activating the virtualenv had a non-zero warning somewhere along the line. But this should have already been fixed by @tomkinsc earlier. So I think it should be safe to remove the set +e +o pipefail that you see peppered in all the apps that require activation of the viral-ngs virtualenv, like here

mlin commented 7 years ago

This should be fixed with #55 but please do reopen if it's seen again