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Add option to pass a file containing list of SNP VCF shard paths #191

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merged 1 commit into from
Jun 28, 2021

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@epiercehoffman epiercehoffman commented Jun 23, 2021

Updates

  • Add File? snp_vcfs_shard_list input as alternative to snp_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 input Array[File] is too long.
  • Update Terra cohort mode dashboard & README to reflect this change
  • Fix broken README link

Testing

  • Validated Module00c WDL & JSON with womtool with both snp_vcfs and snp_vcfs_shard_list inputs
  • Ran test_large through Module00c with default snp_vcfs input as well as snp_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 outputs merged_dels, BAF_stats, and merged_BAF were identical.
  • Will want to confirm this solves the problem observed in the Terra workspace

@epiercehoffman epiercehoffman merged commit c8df307 into master Jun 28, 2021
@epiercehoffman epiercehoffman deleted the eph_pass_snp_vcf_shards_as_text_file branch August 24, 2021 19:47
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