fix: gcnv contig wrapper scripts do not clean their output folders (#443) #468
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…DetermineGermlineContigPloidy runs
…etermineGermlineContigPloidy runs (instead of skipping them) - always purge previous output of GCNV call_cnvs_case_mode step when it's run
…results. This is the cleanest (and least error prone) way of stopping any intermixing with previous results.
Nicolai-vKuegelgen
deleted the
443-gcnv_contig_ploidy-wrapper-script-crahses-because-gatk-determinegermlinecontigploidy-output-is-not-cleaned-but-always-fully-read
branch
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Some of the gcnv step_parts and their associated wrappers create collections of output folders that are currently not tracked by snakemake. Additionally gcnv does only partially overwrite these output files & folders, especially if it is run with fewer samples than in a previous run.
This changes the case_mode wrappers for contig_ploidy and call_cnvs step-parts to always remove the directories they will write into to ensure all output files belong to the current snappy run.
This could be extended to the cohort_mode wrappers, however they might be used in cases where removal of previous samples is not intended, since they could still be relevant (whereas in case mode this is not the case).
Fixes #443