Reduce SVConcordance memory usage #623
Merged
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
VJalili
approved these changes
Jan 2, 2024
inputs/values/dockers.json
Outdated
| @@ -2,7 +2,7 @@ | |||
| "name": "dockers", | |||
| "cnmops_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/cnmops:2023-07-28-v0.28.1-beta-e70dfbd7", | |||
| "condense_counts_docker": "us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-57-g9e03432", | |||
| "gatk_docker": "us.gcr.io/broad-dsde-methods/markw/gatk:2023-07-13-4.4.0.0-43-gd79823f9c-NIGHTLY-SNAPSHOT", | |||
| "gatk_docker": "us.gcr.io/broad-dsde-methods/markw/gatk:mw-sv-concordance-opt-1097258", | |||
There was a problem hiding this comment.
Thank you for updating this image! To keep GCR and ACR in sync, I pushed the updated image to ACR; so could you please update inputs/values/dockers_azure.json with the following image?
vahid.azurecr.io/markw/gatk:mw-sv-concordance-opt-1097258
There was a problem hiding this comment.
Thanks for the reminder here. I have replaced the original branch docker with a gatk nightly build and made sure to push a copy to azure as well.
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Outdated suggestions cannot be applied.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.
Updates WDL and GATK docker for SVConcordance following the GATK update here.
Briefly, SVConcordance memory usage is reduced by sorting the VCF with
bcftoolsrather than performing a sort within the tool itself (GATK does have some neat classes for spilling sorted collections to disk, but they would almost certainly be slower than bcftools for a full vcf sort).Tested successfully on the
hgdpcohort.