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added --preserve-map-align-order #1367

Merged
merged 11 commits into from
Sep 17, 2024
Merged

added --preserve-map-align-order #1367

merged 11 commits into from
Sep 17, 2024

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ekiernan
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Adding a fix for DRAGEN non-determinism back into the DragenAlignment WDL. Scientific tests in comments

@ekiernan
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WGS scientific test: https://gotc-jenkins.dsp-techops.broadinstitute.org/job/warp-workflow-tests/84289/

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🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
WholeGenomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExternalWholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExternalExomeReprocessing.changelog.md has not been changed and needs to be updated
WholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExomeReprocessing.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
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🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
WholeGenomeGermlineSingleSample.wdl has not been changed and needs updating
ExomeGermlineSingleSample.wdl has not been changed and needs updating
ExternalWholeGenomeReprocessing.wdl has not been changed and needs updating
ExternalExomeReprocessing.wdl has not been changed and needs updating
WholeGenomeReprocessing.wdl has not been changed and needs updating
ExomeReprocessing.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

@ekiernan ekiernan closed this Sep 10, 2024
@ekiernan ekiernan reopened this Sep 16, 2024
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Remember to squash merge!

1 similar comment
@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':
WholeGenomeGermlineSingleSample.wdl has not been changed and needs updating
ExomeGermlineSingleSample.wdl has not been changed and needs updating
ExternalWholeGenomeReprocessing.wdl has not been changed and needs updating
ExternalExomeReprocessing.wdl has not been changed and needs updating
WholeGenomeReprocessing.wdl has not been changed and needs updating
ExomeReprocessing.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
Copy link

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
WholeGenomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExternalWholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExternalExomeReprocessing.changelog.md has not been changed and needs to be updated
WholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExomeReprocessing.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

1 similar comment
@github-actions GitHub Actions
Copy link

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
WholeGenomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExternalWholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExternalExomeReprocessing.changelog.md has not been changed and needs to be updated
WholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExomeReprocessing.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

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
WholeGenomeGermlineSingleSample.wdl has not been changed and needs updating
ExomeGermlineSingleSample.wdl has not been changed and needs updating
ExternalWholeGenomeReprocessing.wdl has not been changed and needs updating
ExternalExomeReprocessing.wdl has not been changed and needs updating
WholeGenomeReprocessing.wdl has not been changed and needs updating
ExomeReprocessing.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
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':
WholeGenomeGermlineSingleSample.wdl has not been changed and needs updating
ExomeGermlineSingleSample.wdl has not been changed and needs updating
ExternalWholeGenomeReprocessing.wdl has not been changed and needs updating
ExternalExomeReprocessing.wdl has not been changed and needs updating
WholeGenomeReprocessing.wdl has not been changed and needs updating
ExomeReprocessing.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
Copy link

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
WholeGenomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExternalWholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExternalExomeReprocessing.changelog.md has not been changed and needs to be updated
WholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExomeReprocessing.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
Copy link

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
WholeGenomeGermlineSingleSample.wdl has not been changed and needs updating
ExomeGermlineSingleSample.wdl has not been changed and needs updating
ExternalWholeGenomeReprocessing.wdl has not been changed and needs updating
ExternalExomeReprocessing.wdl has not been changed and needs updating
WholeGenomeReprocessing.wdl has not been changed and needs updating
ExomeReprocessing.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
Copy link

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
WholeGenomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExternalWholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExternalExomeReprocessing.changelog.md has not been changed and needs to be updated
WholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExomeReprocessing.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
Copy link

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
ExomeReprocessing.wdl has not been changed and needs updating
ExternalExomeReprocessing.wdl has not been changed and needs updating
ExternalWholeGenomeReprocessing.wdl has not been changed and needs updating
WholeGenomeReprocessing.wdl has not been changed and needs updating
ExomeGermlineSingleSample.wdl has not been changed and needs updating
WholeGenomeGermlineSingleSample.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
Copy link

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
WholeGenomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExomeGermlineSingleSample.changelog.md has not been changed and needs to be updated
ExternalWholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExternalExomeReprocessing.changelog.md has not been changed and needs to be updated
WholeGenomeReprocessing.changelog.md has not been changed and needs to be updated
ExomeReprocessing.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
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.

1 similar comment
@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.

@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.

@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.

@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.

@ekiernan ekiernan merged commit 1bd7527 into develop Sep 17, 2024
11 checks passed
@ekiernan ekiernan deleted the lk-PD-2748-DRAGEN branch September 17, 2024 19:39
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Reviewers

@kevinpalis kevinpalis kevinpalis approved these changes

@nikellepetrillo nikellepetrillo nikellepetrillo approved these changes

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4 participants
@ekiernan @kevinpalis @nikellepetrillo @actions-user