Closed DarianHole closed 3 years ago
@rdeborja could you look at this?
@DarianHole Previously the workflow would download the MN908947.3
version of the snpEff files from their repository of db build leaving the build_snpeff_db
workflow redundant. Since the latest snpEff update, it looks like the db file is corrupt or the link is broken. I removed the fixed version of snpEff from the script and annotation workflow so that the build will work again. Also, it supports multiple installed versions of snpEff in a single conda environment. I have added branch fix_snpeff_build
to address this and submitted a PR. Feel free to try out the branch and let me know if you run into any issues.
@DarianHole the branch has been merged and should resolve the db build issue.
Awesome, thanks! I'll run it through right now and update you with the results
Works as intended! Thanks again for the quick fixes to this and the snpEFF logs
SnpEFF seems to have updated to a new version
5.0-1
which is causing the database build to fail when it is installed instead of version5.0-0
.Likely due to the line here as given to me by @kdmack87: https://github.com/jts/ncov-tools/blob/21fd71f4fc9207a592d6684997d6b66bc2d4ad3a/workflow/scripts/build_db.py#L9
I am not sure if the best solution would be to specify multiple options in the above file or to set the environment dependency to be exactly
5.0-0
(not sure if conda allows the-
in the environment files for a version number?)I worked around this by going into my conda environment and re-naming the folder from
5.0-1
to5.0-0
, building the database, and then re-naming it back but that is not super ideal. Once I did this everything else still worked as intended