Add option to pass a file containing list of SNP VCF shard paths #191
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Outdated suggestions cannot be applied.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
File? snp_vcfs_shard_list
input as alternative tosnp_vcfs
. This input is a GCS path to a text file containing a list of paths to SNP VCF shards (one per line). We are hoping to circumvent a Terra issue that arises if an inputArray[File]
is too long.Testing
snp_vcfs
andsnp_vcfs_shard_list
inputstest_large
throughModule00c
with defaultsnp_vcfs
input as well assnp_vcfs_shard_list
and verified that the workflow cached most of the way through (a few steps in CNMOPS, bincov, and EvidenceMerging didn't cache but all the BAF steps did) and that the outputsmerged_dels
,BAF_stats
, andmerged_BAF
were identical.