Pd 2898 deprecate pipelines by nikellepetrillo · Pull Request #1541 · broadinstitute/warp

nikellepetrillo · 2025-03-10T17:17:31Z

Description

This PR moves deprecated pipelines (and their associated test inputs, test wdls, and verification wdls) into a deprecated folder.

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?

* deprecating rna with umis and annotation filtration

* deprecate * unnested dna_seq * chr1 * deprecation notices --------- Co-authored-by: ekiernan <ekiernan@broadinstitute.org>

…ns.txt (#1539) * remove deprecated pipelines from .dockstore.yml * remove deprecated pipelines from pipeline_versions.txt * alpabetical order .dockstore.yml

github-actions · 2025-03-10T17:17:44Z

Remember to squash merge!

github-actions · 2025-03-10T17:17:54Z

🔍Version Validation Results:

grep: pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.wdl: No such file or directory
Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-03-10T17:18:09Z

🔍Changelog Validation Results:

grep: pipelines/skylab/smartseq2_single_sample/SmartSeq2SingleSample.wdl: No such file or directory
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

* deprecate MultiSampleSmartSeq2 * Updated pipeline_versions.txt with all pipeline version information * Update pipeline_versions.txt --------- Co-authored-by: GitHub Action <action@github.com> Co-authored-by: Nikelle Petrillo <38223776+nikellepetrillo@users.noreply.github.com>

github-actions · 2025-03-10T17:21:20Z

Remember to squash merge!

github-actions · 2025-03-10T17:21:30Z

🔍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 · 2025-03-10T17:21:31Z

🔍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 · 2025-03-10T17:25:03Z

Remember to squash merge!

github-actions · 2025-03-10T17:25:13Z

🔍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 · 2025-03-10T17:25:15Z

🔍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 · 2025-03-10T17:28:02Z

Remember to squash merge!

github-actions · 2025-03-10T17:28:10Z

🔍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 · 2025-03-10T17:29:17Z

Remember to squash merge!

github-actions · 2025-03-10T17:29:27Z

🔍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 · 2025-03-10T17:29:27Z

🔍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 · 2025-03-10T17:43:37Z

🔍Changelog Validation Results:

…o PD-2898-deprecate-pipelines

github-actions · 2025-03-10T18:35:15Z

Remember to squash merge!

github-actions · 2025-03-10T18:35:27Z

🔍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 · 2025-03-10T18:35:28Z

🔍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 · 2025-03-10T18:38:47Z

Remember to squash merge!

github-actions · 2025-03-10T18:38:57Z

🔍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 · 2025-03-10T18:38:57Z

🔍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 · 2025-03-11T17:30:14Z

Remember to squash merge!

github-actions · 2025-03-11T17:30:24Z

🔍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 · 2025-03-11T17:30:26Z

🔍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 · 2025-03-11T17:33:50Z

Remember to squash merge!

github-actions · 2025-03-11T17:33:58Z

🔍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.

github-actions · 2025-03-11T17:34:02Z

🔍Changelog Validation Results:

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

ekiernan and others added 14 commits March 6, 2025 10:47

Deprecating AnnotationFiltration and BroadInternalRNAWithUMIs (#1523)

0ba0ac0

* deprecating rna with umis and annotation filtration

deprecate BroadInternalImputation.wdl (#1524)

1816960

Deprecate BroadInternalUltimaGenomics (#1525)

4937bfb

Deprecate JointGenotypingByChromosome (#1530)

58d1fc5

* deprecate * unnested dna_seq * chr1 * deprecation notices --------- Co-authored-by: ekiernan <ekiernan@broadinstitute.org>

deprecate BroadInternal Arrays (#1527)

604b2bf

Np deprecate scatac (#1531)

dbd5eec

deprecated CheckFingerprint (#1526)

8e97c0c

Pd 2898 deprecatesid -arrays (#1528)

18a93b1

deprecate External WGS Reprocessing (#1532)

2eecac4

deprecate SmartSeq2SingleSample (#1533)

9ef4475

deprecate ExternalExomeReprocessing.wdl (#1534)

85e9757

deprecated the ValidateChip pipeline (#1535)

1220a25

deprecate MultiSampleArrays.wdl (#1536)

2e9e3fd

Np remove deprecated pipelines from dockstore.yml and pipeline_versio…

e809d74

…ns.txt (#1539) * remove deprecated pipelines from .dockstore.yml * remove deprecated pipelines from pipeline_versions.txt * alpabetical order .dockstore.yml

Updated pipeline_versions.txt with all pipeline version information

342c211

Updated pipeline_versions.txt with all pipeline version information

19e54e7

move biobambam2 into deprecated

1d1d67f

move biobambam2 into deprecated

9016c36

Merge branch 'develop' into PD-2898-deprecate-pipelines

4c33e57

nikellepetrillo added 2 commits March 10, 2025 14:34

skip deprecated wdls in womtools check

7c71122

Merge remote-tracking branch 'origin/PD-2898-deprecate-pipelines' int…

0678713

…o PD-2898-deprecate-pipelines

skip tests dir in womtools check

d1bff37

khajoue2 approved these changes Mar 10, 2025

View reviewed changes

jessicaway approved these changes Mar 10, 2025

View reviewed changes

Merge branch 'develop' into PD-2898-deprecate-pipelines

209093c

Update validate_wdls.sh

fde4f40

nikellepetrillo merged commit 784c460 into develop Mar 11, 2025
10 checks passed

ekiernan deleted the PD-2898-deprecate-pipelines branch November 20, 2025 20:35

claymcleod mentioned this pull request Apr 11, 2026

fix: update broken relative imports in deprecated pipelines #1813

Closed

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nikellepetrillo commented Mar 10, 2025

Description

This PR moves deprecated pipelines (and their associated test inputs, test wdls, and verification wdls) into a deprecated folder.

Checklist

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