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v0.28-beta

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@epiercehoffman epiercehoffman released this 27 Jun 16:20
· 169 commits to main since this release
v0.28-beta
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Learn about vigilant mode.

Note: This version corresponding to v0.28-beta does not have updated docker images. The docker image updates are now reflected in v0.28.1-beta so that version should be used instead.

What's changed

Improvements to SR genotyping and INS breakpoints:

  • Update SR counting and genotyping

Filtering workflows:

  • Update ApplyManualVariantFilter json template
  • Update VaPoR workflows
  • SVConcordance workflows update
  • Fix CTX END2 error in GATK formatting script

Other workflows:

  • Fix non-deterministic errors in GetSampleIdsFromVcfTar
  • make the RunMELT task a little more robust
  • Improve STR workflow
  • Remove DeleteIntermediateFiles task
  • Remove unused ped_file input from GenotypeBatch and RegenotypeCNVs

Docker build:

  • Manually install MASS R package in sv-pipeline-virtual-env
  • Build and publish images to multiple registries in one job, & update the dependencies of the action

Other scripts, docs, and JSONs:

  • Update copy_outputs.py
  • Generate Terra workspace tsv files from transposed tables
  • Update README to link to SV callers used
  • Remove ped file from workspace data TSV for cohort mode terra workspace

Full Changelog: v0.27.3-beta...v0.28-beta

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