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Follow up to 2nd round of gnomAD MakeCohortVcf updates #290

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merged 3 commits into from
Feb 3, 2022
Merged

Follow up to 2nd round of gnomAD MakeCohortVcf updates #290

merged 3 commits into from
Feb 3, 2022

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epiercehoffman
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@epiercehoffman epiercehoffman commented Feb 2, 2022 •
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Updates

  • Remove inputs for deleted CleanVcf tasks GetSampleIDsFromVcf and SubsetPedFile from single-sample WDL. Follow-up to Second round of MakeCohortVcf updates from gnomAD #288 to get WDLs to validate.
  • Change spaces to tabs for new entries in Terra workspace.tsv templates.
  • Add back call to sanitize_filter_field.py at the end of CleanVcfChromosome.

Testing

  • Validated all WDLs and JSONs with womtool.
  • Uploaded workspace.tsv tables to Terra successfully.
  • Successfully ran MakeCohortVcf in Terra on my branch on two 1KGP batches, with updated workspace data table and inputs.

@epiercehoffman epiercehoffman changed the title Remove inputs for deleted task from single sample WDL Follow up to 2nd round of gnomAD MakeCohortVcf updates Feb 3, 2022
@epiercehoffman epiercehoffman merged commit ab8a855 into master Feb 3, 2022
@mwalker174 mwalker174 deleted the eph_follow_up_validate_288 branch February 3, 2022 20:32
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@mwalker174 mwalker174 mwalker174 approved these changes

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@epiercehoffman @mwalker174