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Option to input & subset multi-sample BED in VaPoR (+ womtool fixes) #409

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merged 2 commits into from
Sep 19, 2022

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@epiercehoffman epiercehoffman commented Sep 16, 2022

Updates

  • Option to provide multi-sample instead of single-sample BED file for VaPoR input - users should then provide a sample ID to extract from the multi-sample BED file before the VaPoR tool is invoked. Allows users to use the cohort-wide BED file produced by MainVcfQc directly
  • Style edits in VaPoR WDLs: spacing, make VCF / BED file required in file-specific WDLs
  • Various womtool fixes to get validation to run with validation script (tested with womtool-80)

Testing

  • Womtool validation of all WDLs and JSONs
  • Tested VaPoR on Terra with multi-sample BED file + sample ID to extract
  • Tested VaPoR on Terra with single-sample BED file - output identical to previous master

@epiercehoffman epiercehoffman merged commit 90e3e9a into master Sep 19, 2022
@epiercehoffman epiercehoffman deleted the eph_vapor_subset_multisample_bed branch September 19, 2022 17:05
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