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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:
Have enaDataGet throw an exception and abort with non-zero exit code
Add a sanity check after download. Perhaps something basic like gzip -t or maybe fq lint
The text was updated successfully, but these errors were encountered:
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:
gzip -t
or maybefq lint
The text was updated successfully, but these errors were encountered: