Update HaplotypeCaller_GATK4_VCF to use MEM_SIZE and MEM_UNIT by nikellepetrillo · Pull Request #1515 · broadinstitute/warp

nikellepetrillo · 2025-02-21T14:11:14Z

Description

Give your PR a concise yet descriptive title.
Please explain the changes you made here.
Explain the motivation for making this change. What existing problem does the pull request solve?
Mention any issues fixed, addressed, or otherwise related to this pull request, including issue numbers or hard links for issues in other repos.
You can delete these instructions once you have written your PR description.

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 · 2025-02-21T14:11:28Z

Remember to squash merge!

github-actions · 2025-02-21T14:11:37Z

🔍Version Validation Results:

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

github-actions · 2025-02-21T14:11:40Z

🔍Changelog Validation Results:

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

github-actions · 2025-02-21T18:11:53Z

Remember to squash merge!

github-actions · 2025-02-21T18:12:00Z

🔍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 · 2025-02-21T18:12:02Z

🔍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 · 2025-02-21T18:24:18Z

Remember to squash merge!

github-actions · 2025-02-21T18:24:23Z

🔍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 · 2025-02-21T18:24:24Z

🔍Changelog Validation Results:

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

ekiernan

lgtm! ty!

github-actions · 2025-02-28T13:55:55Z

Remember to squash merge!

github-actions · 2025-02-28T13:56:04Z

🔍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 · 2025-02-28T13:56:06Z

🔍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 · 2025-02-28T13:57:37Z

Remember to squash merge!

github-actions · 2025-02-28T13:57:46Z

🔍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 · 2025-02-28T13:57:48Z

🔍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 · 2025-03-12T13:46:06Z

Remember to squash merge!

github-actions · 2025-03-12T13:46:17Z

🔍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 · 2025-03-12T13:46:17Z

🔍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 · 2025-03-12T13:47:35Z

Remember to squash merge!

github-actions · 2025-03-12T13:47:44Z

🔍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 · 2025-03-12T13:47:49Z

🔍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 · 2025-03-12T13:53:20Z

Remember to squash merge!

github-actions · 2025-03-12T13:53:29Z

🔍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 · 2025-03-12T13:53:30Z

🔍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 · 2025-03-12T13:54:30Z

Remember to squash merge!

github-actions · 2025-03-12T13:54:37Z

🔍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 · 2025-03-12T13:54:40Z

🔍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.

jessicaway

looks good, thanks @nikellepetrillo!

github-actions · 2025-03-14T22:01:13Z

Remember to squash merge!

github-actions · 2025-03-14T22:01:20Z

🔍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 · 2025-03-14T22:01:22Z

🔍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.

Update HaplotypeCaller_GATK4_VCF to use MEM_SIZE and MEM_UNIT

8d7947b

changelogs

699d681

Updated pipeline_versions.txt with all pipeline version information

99aedad

nikellepetrillo added 2 commits February 21, 2025 13:23

changelogs

173d7a4

Merge remote-tracking branch 'origin/np_mem_unit' into np_mem_unit

31075d3

ekiernan approved these changes Feb 24, 2025

View reviewed changes

Merge branch 'develop' into np_mem_unit

344f3a1

Updated pipeline_versions.txt with all pipeline version information

ed465e9

nikellepetrillo added 2 commits February 28, 2025 08:57

dummy commit

5525090

Merge remote-tracking branch 'origin/np_mem_unit' into np_mem_unit

657a324

merge conflicts

a836d6a

Updated pipeline_versions.txt with all pipeline version information

b60bfcf

nikellepetrillo added 2 commits March 12, 2025 09:47

merge conflicts

9fe5f07

Merge remote-tracking branch 'origin/np_mem_unit' into np_mem_unit

56bebad

merge conflicts

9416ebb

merge conflicts

3111287

jessicaway approved these changes Mar 12, 2025

View reviewed changes

dummy commit

53ce0f8

nikellepetrillo merged commit 1453fe1 into develop Mar 17, 2025
18 checks passed

nikellepetrillo mentioned this pull request Mar 17, 2025

Update HaplotypeCaller_GATK4_VCF to use MEM_SIZE and MEM_UNIT #1448

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nikellepetrillo commented Feb 21, 2025

Description

Checklist

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github-actions bot commented Feb 21, 2025

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github-actions bot commented Feb 21, 2025

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github-actions bot commented Feb 28, 2025

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🔍Changelog Validation Results:

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🔍Version Validation Results:

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github-actions bot commented Feb 28, 2025

🔍Version Validation Results:

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github-actions bot commented Feb 28, 2025

🔍Changelog Validation Results:

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github-actions bot commented Mar 12, 2025

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github-actions bot commented Mar 12, 2025

🔍Changelog Validation Results:

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github-actions bot commented Mar 12, 2025

🔍Version Validation Results:

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github-actions bot commented Mar 12, 2025

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github-actions bot commented Mar 12, 2025

🔍Version Validation Results:

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github-actions bot commented Mar 12, 2025

🔍Changelog Validation Results:

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github-actions bot commented Mar 12, 2025

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github-actions bot commented Mar 12, 2025

🔍Version Validation Results:

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github-actions bot commented Mar 12, 2025

🔍Changelog Validation Results:

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github-actions bot commented Mar 12, 2025

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github-actions bot commented Mar 12, 2025

🔍Changelog Validation Results:

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github-actions bot commented Mar 12, 2025

🔍Version Validation Results:

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