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  • Handle arrays of length zero as clustered VCF inputs to JoinRawCalls. There are 6 different clustered VCF inputs for the different algorithms, and our input configurations provide all of them so that users don't have to edit them depending on which callers were used. But Terra translates an empty column to an empty array [] rather than a null value, so merely using select_all doesn't produce the expected results. This causes JoinRawCalls to fail with the default input configuration
  • Add clustered MELT VCFs to the default input configuration - although MELT is now deprecated, users processing legacy data with MELT calls should include them when running JoinRawCalls

Testing

  • Validated WDLs and JSONs with womtool and Terra validation script
  • Ran JoinRawCalls on one cohort, pointing to empty columns for DRAGEN and MELT VCFs. The run succeeded - but note that the cohort was only one batch, so I am relying on previous testing for the success of the multi-batch logic

Notes

  • Need to revert dockstore.yml before merging
  • Need to merge before next release

@epiercehoffman epiercehoffman added the bug Something isn't working label Sep 2, 2025
@epiercehoffman epiercehoffman merged commit 4fdac8f into main Sep 4, 2025
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@epiercehoffman epiercehoffman deleted the eph_empty_lists_joinrawcalls branch September 4, 2025 15:15
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