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updates to BGE joint calling pipeline from GVS tieout #1370

Merged
merged 7 commits into from
Sep 16, 2024
Merged

updates to BGE joint calling pipeline from GVS tieout #1370

merged 7 commits into from
Sep 16, 2024

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meganshand
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While tying out the BGE joint calling pipeline on GVS, two differences from the WARP pipeline implementation came up that should be updated here to match what we decided to do in GVS.

  1. The VETS filtering model should be trained on the variants only in the target regions, but should be applied to all variants output by the pipeline (including the hard filtered ones). This is added with the --ignore-all-filters optional argument which is shown in the bge inputs json.
  2. We added the ability to add a description to the OUTSIDE_OF_TARGETS filter for the header of the output VCF in GATK 4.6.0.0 which can now be added to the HardFilterAndMakeSitesOnly task if the targets are provided as an optional input.

This is expected to change one scientific test (the bge specific run of JointGenotyping), but all plumbing tests should pass.

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🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
JointGenotypingByChromosomePartTwo.changelog.md has not been changed and needs to be updated
JointGenotypingByChromosomePartOne.changelog.md has not been changed and needs to be updated
UltimaGenomicsJointGenotyping.changelog.md has not been changed and needs to be updated
JointGenotyping.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

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🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
JointGenotypingByChromosomePartTwo.wdl has not been changed and needs updating
JointGenotypingByChromosomePartOne.wdl has not been changed and needs updating
UltimaGenomicsJointGenotyping.wdl has not been changed and needs updating
JointGenotyping.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

@github-actions GitHub Actions
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Remember to squash merge!

@github-actions GitHub Actions
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🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
JointGenotypingByChromosomePartTwo.wdl has not been changed and needs updating
JointGenotypingByChromosomePartOne.wdl has not been changed and needs updating
UltimaGenomicsJointGenotyping.wdl has not been changed and needs updating
JointGenotyping.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

@github-actions GitHub Actions
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🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
JointGenotypingByChromosomePartTwo.changelog.md has not been changed and needs to be updated
JointGenotypingByChromosomePartOne.changelog.md has not been changed and needs to be updated
UltimaGenomicsJointGenotyping.changelog.md has not been changed and needs to be updated
JointGenotyping.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

@github-actions GitHub Actions
Copy link

Remember to squash merge!

@github-actions GitHub Actions
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🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

@github-actions GitHub Actions
Copy link

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

@meganshand
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retest this please

@meganshand
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Scientific test for JointGenotyping is here: https://gotc-jenkins.dsp-techops.broadinstitute.org/job/warp-workflow-tests/84485/

The only failure is the expected BGE differences and I looked at the output and all the differences were as expected.

@github-actions GitHub Actions
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Remember to squash merge!

@github-actions GitHub Actions
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🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

@github-actions GitHub Actions
Copy link

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

@github-actions GitHub Actions
Copy link

Remember to squash merge!

@github-actions GitHub Actions
Copy link

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

@github-actions GitHub Actions
Copy link

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

@meganshand @ekiernan
Update changelog docs
1a60e3a 
Co-authored-by: ekiernan <[email protected]>
@github-actions GitHub Actions
Copy link

Remember to squash merge!

@github-actions GitHub Actions
Copy link

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

@github-actions GitHub Actions
Copy link

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

@meganshand meganshand merged commit fe21c07 into develop Sep 16, 2024
9 of 11 checks passed
@meganshand meganshand deleted the ms_bge_filtering branch September 16, 2024 14:26
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@ekiernan ekiernan ekiernan approved these changes

@nikellepetrillo nikellepetrillo nikellepetrillo approved these changes

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@meganshand @nikellepetrillo @ekiernan @actions-user