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ena download does not throw an exception when download fails #1

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SichongP opened this issue Apr 8, 2021 · 0 comments
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ena download does not throw an exception when download fails #1

SichongP opened this issue Apr 8, 2021 · 0 comments
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@SichongP
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SichongP commented Apr 8, 2021

As mentioned in enasequence/enaBrowserTools#42, the tool used to fetch ENA data does not throw an exception when download fails. This causes Snakemake to interpret job as having completed successfully, which then causes errors in downstream step mergeFASTQ.

We can either:

  1. Have enaDataGet throw an exception and abort with non-zero exit code
  2. Add a sanity check after download. Perhaps something basic like gzip -t or maybe fq lint
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