[TSPS-770] Update Beagle jar to remove trailing zeros from AF and DR2 annotations by salonishah11 · Pull Request #1747 · broadinstitute/warp

salonishah11 · 2026-01-16T20:04:34Z

Description

Jira: https://broadworkbench.atlassian.net/browse/TSPS-770

This PR updates Phase and Impute tasks docker image to remove trailing zeros from AF and DR2 annotations in the output VCF.
Warp-tools PR: broadinstitute/warp-tools#180

Checklist

If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP team by tagging @broadinstitute/warp-admins in a comment on this PR.

Did you add inputs, outputs, or tasks to a workflow?
Did you modify, delete or move: file paths, file names, input names, output names, or task names?
If you made a changelog update, did you update the pipeline version number?

github-actions · 2026-01-16T20:04:43Z

Remember to squash merge!

github-actions · 2026-01-16T20:04:54Z

🔍Changelog Validation Results:

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

github-actions · 2026-01-16T20:04:55Z

🔍Version Validation Results:

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

github-actions · 2026-01-21T20:58:00Z

Remember to squash merge!

github-actions · 2026-01-21T20:58:11Z

🔍Version Validation Results:

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

github-actions · 2026-01-21T20:58:12Z

🔍Changelog Validation Results:

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

github-actions · 2026-01-22T22:54:06Z

Remember to squash merge!

github-actions · 2026-01-22T22:54:16Z

🔍Version Validation Results:

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

github-actions · 2026-01-22T22:54:16Z

🔍Changelog Validation Results:

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

github-actions · 2026-01-23T18:48:08Z

Remember to squash merge!

github-actions · 2026-01-23T18:48:17Z

🔍Version Validation Results:

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

github-actions · 2026-01-23T18:48:18Z

🔍Changelog Validation Results:

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

github-actions · 2026-01-27T14:43:33Z

Remember to squash merge!

github-actions · 2026-01-27T14:43:47Z

🔍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 · 2026-01-27T14:43:47Z

🔍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 · 2026-01-27T14:45:47Z

Remember to squash merge!

github-actions · 2026-01-27T14:45:58Z

🔍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 · 2026-01-27T14:45:58Z

🔍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.

salonishah11 · 2026-01-27T20:54:59Z

The failing test is expected because there is a slight change in how AF and DR2 annotations are written in vcf file. Once this PR merges I will run the GHA to update the truth data.

mmorgantaylor · 2026-01-27T21:17:25Z

+2026-01-27 (Date of Last Commit)
+
+* Updates Phase and Impute tasks docker image to remove trailing zeros from AF and DR2 annotations in the output VCF. 
+The Beagle JAR is generated from GitHub repo [tmp-sharing/imp-server](https://github.com/tmp-sharing/imp-server/tree/master).


I don't think we need to include this, since it was already part of the 2.4.0 version description

Sounds good, I will remove the Github repo part 👍

github-actions · 2026-01-27T21:29:17Z

Remember to squash merge!

github-actions · 2026-01-27T21:29:26Z

🔍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 · 2026-01-27T21:29:28Z

🔍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 · 2026-01-27T21:29:48Z

Remember to squash merge!

github-actions · 2026-01-27T21:29:59Z

🔍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 · 2026-01-27T21:30:01Z

🔍Changelog Validation Results:

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

update beagle to test image w/o trailing zeroes

7b06497

use Brian's version of removing trailing 0s

4244bc1

remove compression logic to see what fails

f8cf205

making sure the right hash is used for Beagle image

367111a

remove test changes; use final docker image; update documentation

f6189ec

Updated pipeline_versions.txt with all pipeline version information

9d4d874

salonishah11 marked this pull request as ready for review January 27, 2026 14:45

Merge branch 'develop' into sps_beagle_no_trailing_zeroes

c0798f4

mmorgantaylor approved these changes Jan 27, 2026

View reviewed changes

Merge branch 'develop' into sps_beagle_no_trailing_zeroes

970cf68

PR feedback

5ac2e16

rsc3 approved these changes Jan 27, 2026

View reviewed changes

salonishah11 merged commit 8cfb509 into develop Jan 28, 2026
10 of 11 checks passed

salonishah11 deleted the sps_beagle_no_trailing_zeroes branch January 28, 2026 14:51

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salonishah11 commented Jan 16, 2026 •

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