Integrate ReshardVcf into ResolveComplexVariants #626
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
epiercehoffman
approved these changes
May 28, 2024
| File contig_list | ||
| String prefix | ||
| Boolean? use_ssd | ||
| String sv_base_mini_docker | ||
| RuntimeAttr? runtime_override_reshard | ||
| } | ||
|
|
||
| Array[String] contigs = read_lines(contig_list) | ||
| Array[String] contigs = transpose(read_tsv(contig_list))[0] |
There was a problem hiding this comment.
Make sure to update the ReshardVcf JSON templates (test & terra) to use the primary_contigs_fai to match this change - it looks like it was initially set up with primary_contigs_list
There was a problem hiding this comment.
It runs ok with the contigs list too
mwalker174
force-pushed
the
mw_vcf_reshard
branch
from
6789cd2
to
22ae6c5
Compare
Add json template Update top-level workflows; concat variant lists Fix contig list read Update ref panel outputs; fix CleanVcf template Fix Terra CleanVcf templates
mwalker174
force-pushed
the
mw_vcf_reshard
branch
from
22ae6c5
to
2dc6b11
Compare
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Outdated suggestions cannot be applied.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.
Adds a call to
ReshardVcfat the end ofResolveComplexVariants. In addition, each of theBOTHSIDES_PASSandHIGH_SR_BACKGROUNDcontig-sharded variant tables is concatenated into a single genome-wide table prior to annotating records with these flags inCleanVcf. This has a slight cost in memory footprint inCleanVcf1abut ensures that shuffled records are properly annotated. Json templates and top-level workflows are also updated.This branch was successfully tested on
ResolveComplexVariants,GenotypeComplexVariants,andCleanVcf.