Update docker - Githubissues

DataBiosphere / analysis_pipeline_WDL

Collection of WDL workflows based off the University of Washington TOPMed DCC Best Practices for GWAS. The WDL structure was based upon CWLs written by the Seven Bridges development team.

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Update docker #79

Closed aofarrel closed 2 years ago

aofarrel commented 2 years ago

Update Docker image to uwgac/topmed-master:2.12.1 (checker workflow exited successfully on old inputs)
Better scaling on the segment preparation task for some use cases -- now scales on n_segments, but this isn't helpful if segment length is used instead of n_segments
Debug prints are now on by default in association aggregate task
Clarify that prepare segments python code is for python 2 due to how it handles unicode stuff

aofarrel commented 2 years ago

Something changed in the new Docker and it seems those changes might not be on GitHub, so I can't easily tell what they are. Stephanie is OOO at the moment so it's best to move these changes, sans the Docker update, to another PR.

aofarrel commented 2 years ago

Actually it seems like supposed Docker changes might have just been a side effect of the pipefail (correctly) firing when assoc_agg couldn't handle my slightly bogus input file... will keep this separate for now regardless.