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Pd 2898 deprecatesid -arrays#1528

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ekiernan merged 4 commits intoPD-2898-deprecate-pipelinesfrom
PD-2898-deprecatesid
Mar 6, 2025
Merged

Pd 2898 deprecatesid -arrays#1528
ekiernan merged 4 commits intoPD-2898-deprecate-pipelinesfrom
PD-2898-deprecatesid

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@rsc3 rsc3 commented Mar 6, 2025

Description

depreacting the single sample Arrays pipeline

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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?

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github-actions bot commented Mar 6, 2025

Remember to squash merge!

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github-actions bot commented Mar 6, 2025

🔍Changelog Validation Results:

grep: pipelines/broad/arrays/single_sample/Arrays.wdl: No such file or directory
Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
BroadInternalArrays.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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github-actions bot commented Mar 6, 2025

🔍Version Validation Results:

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

@jessicaway jessicaway changed the base branch from develop to PD-2898-deprecate-pipelines March 6, 2025 16:20
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github-actions bot commented Mar 6, 2025

🔍Changelog Validation Results:

grep: pipelines/broad/arrays/single_sample/Arrays.wdl: No such file or directory
Comparing changelogs for pipelines that differ from the versions on 'origin/PD-2898-deprecate-pipelines':
BroadInternalArrays.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

@ekiernan ekiernan merged commit 18a93b1 into PD-2898-deprecate-pipelines Mar 6, 2025
0 of 3 checks passed
nikellepetrillo added a commit that referenced this pull request Mar 11, 2025
* Deprecating AnnotationFiltration and BroadInternalRNAWithUMIs (#1523)

* deprecating rna with umis and annotation filtration

* deprecate BroadInternalImputation.wdl (#1524)

* Deprecate BroadInternalUltimaGenomics (#1525)

* Deprecate JointGenotypingByChromosome (#1530)

* deprecate

* unnested dna_seq

* chr1

* deprecation notices

---------

Co-authored-by: ekiernan <ekiernan@broadinstitute.org>

* deprecate BroadInternal Arrays (#1527)

* Np deprecate scatac (#1531)

* deprecated CheckFingerprint (#1526)

* Pd 2898 deprecatesid -arrays (#1528)

* deprecate External WGS Reprocessing (#1532)

* deprecate SmartSeq2SingleSample (#1533)

* deprecate ExternalExomeReprocessing.wdl (#1534)

* deprecated the ValidateChip pipeline (#1535)

* deprecate MultiSampleArrays.wdl (#1536)

* Np remove deprecated pipelines from dockstore.yml and pipeline_versions.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

* Pd 2898 jw  deprecate multisample ss2 (#1537)

* 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>

* Updated pipeline_versions.txt with all pipeline version information

* move biobambam2 into deprecated

* move biobambam2 into deprecated

* skip deprecated wdls in womtools check

* skip tests dir in womtools check

* Update validate_wdls.sh

---------

Co-authored-by: Elizabeth Kiernan <55763654+ekiernan@users.noreply.github.com>
Co-authored-by: aawdeh <awdeh@broadinstitute.org>
Co-authored-by: ekiernan <ekiernan@broadinstitute.org>
Co-authored-by: Jessica Way <jway@broadinstitute.org>
Co-authored-by: Robert Sidney Cox <sidcox@broadinstitute.org>
Co-authored-by: GitHub Action <action@github.com>
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5 participants