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epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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Add artic minion logging for debugging #105

Closed ammaraziz closed 3 months ago

ammaraziz commented 8 months ago

I've had a few issues with the artic minion command in the run_artic.sh. One issue is the mock_artic bash function essentially acts as a silencer if the artic minion pipeline fails. Unfortunately, if there's an issue this makes debugging impossible. See for example my other issue #104

mattdmem commented 3 months ago

Sorry - I know you submitted this PR ages ago. We're going to implement this log file. Thanks for your suggestion.

Matt

bede commented 3 months ago

Hi Ammar, in the next release a log file containing stdout and stderr will be included in the output directory as {barcode}.artic.log.txt. If for some reason the pipeline terminates before these logs are published into the output directory, they can be found inside the work dir using e.g.

find work -name "*.artic.log.txt"