PD-2945: Update slide-tags #1567

aawdeh · 2025-04-11T15:29:07Z

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?

… develop

github-actions · 2025-04-11T15:29:19Z

Remember to squash merge!

github-actions · 2025-04-11T15:29:29Z

🔍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 · 2025-04-11T15:29:33Z

🔍Changelog Validation Results:

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

github-actions · 2025-04-11T15:37:39Z

Remember to squash merge!

github-actions · 2025-04-11T15:37:47Z

🔍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 · 2025-04-11T15:37:48Z

🔍Changelog Validation Results:

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

github-actions · 2025-04-11T15:38:18Z

Remember to squash merge!

github-actions · 2025-04-11T15:38:26Z

🔍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 · 2025-04-11T15:38:27Z

🔍Changelog Validation Results:

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

github-actions · 2025-04-11T16:12:06Z

Remember to squash merge!

github-actions · 2025-04-11T16:12:14Z

🔍Changelog Validation Results:

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

github-actions · 2025-04-11T16:12:16Z

🔍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 · 2025-04-11T16:14:37Z

Remember to squash merge!

github-actions · 2025-04-11T16:14:48Z

🔍Changelog Validation Results:

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

github-actions · 2025-04-11T16:14:49Z

🔍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 · 2025-04-14T17:09:26Z

Remember to squash merge!

github-actions · 2025-04-14T17:09:35Z

🔍Changelog Validation Results:

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

github-actions · 2025-04-14T17:09:36Z

🔍Version Validation Results:

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

github-actions · 2025-04-14T17:10:03Z

Remember to squash merge!

github-actions · 2025-04-14T17:10:13Z

🔍Version Validation Results:

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

github-actions · 2025-04-16T20:36:36Z

🔍Changelog Validation Results:

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

…into aa-slidetag

github-actions · 2025-04-16T20:37:54Z

Remember to squash merge!

github-actions · 2025-04-16T20:38:01Z

🔍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 · 2025-04-16T20:38:05Z

🔍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 · 2025-04-16T20:41:05Z

Remember to squash merge!

github-actions · 2025-04-16T20:41:17Z

🔍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 · 2025-04-16T20:41:17Z

🔍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 · 2025-04-22T14:47:02Z

Remember to squash merge!

github-actions · 2025-04-22T14:47:11Z

🔍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 · 2025-04-22T14:47:20Z

🔍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 · 2025-04-23T13:23:26Z

Remember to squash merge!

github-actions · 2025-04-23T13:23:37Z

🔍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 · 2025-04-23T13:23:42Z

🔍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 · 2025-04-23T16:14:54Z

Remember to squash merge!

github-actions · 2025-04-23T16:15:05Z

🔍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 · 2025-04-23T16:15:06Z

🔍Changelog Validation Results:

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

* PD-2945: Update slide-tags (#1567) * Np add tests peakcalling (#1578) * add peakcalling test * add peakcalling test * add peakcalling test * turn call caching off * turn call caching off * turn call caching off * turn call caching off * update input for peakcalling * add sci test for peakcalling (#1580) * add sci test for peakcalling * add sci test for peakcalling * add sci test for peakcalling * PD-2937: Update BestPractices.md (#1584) * PD-2950: Write up SlideTags documentation (#1581) * Rc 2880 warp and forking (#1586) * update WARP name * update WARP name * Document on Forking WARP and pushing to dockstore * Updated pipeline_versions.txt with all pipeline version information --------- Co-authored-by: Farzaneh Khajouei <[email protected]> Co-authored-by: GitHub Action <[email protected]> * update to new input paths * Updated pipeline_versions.txt with all pipeline version information * Updated pipeline_versions.txt with all pipeline version information * update to new input paths * temp copy sci inputs to plumbing for testing purposes only * PD-2939: Add philosophy section to the get-started page (#1587) * fix paths * fix paths * fix paths * fix paths * rearrange input json * update truth bucket interpretation logic * dont cancel runs for now * up memory in CollectAggregationMetrics * mor emem * mor emem * remove jsons * remove jsons --------- Co-authored-by: aawdeh <[email protected]> Co-authored-by: Robert Sidney Cox <[email protected]> Co-authored-by: Farzaneh Khajouei <[email protected]> Co-authored-by: GitHub Action <[email protected]>

* PD-2945: Update slide-tags (#1567) * Np add tests peakcalling (#1578) * add peakcalling test * add peakcalling test * add peakcalling test * turn call caching off * turn call caching off * turn call caching off * turn call caching off * update input for peakcalling * add sci test for peakcalling (#1580) * add sci test for peakcalling * add sci test for peakcalling * add sci test for peakcalling * PD-2937: Update BestPractices.md (#1584) * PD-2950: Write up SlideTags documentation (#1581) * Rc 2880 warp and forking (#1586) * update WARP name * update WARP name * Document on Forking WARP and pushing to dockstore * Updated pipeline_versions.txt with all pipeline version information --------- Co-authored-by: Farzaneh Khajouei <[email protected]> Co-authored-by: GitHub Action <[email protected]> * PD-2939: Add philosophy section to the get-started page (#1587) * updated run_ancestry population metadata tsv and filtering parameters (#1590) * RNA-seq alignment pipeline for All of Us * add macaque test input json (#1593) * add macaque test input json * Updated pipeline_versions.txt with all pipeline version information * add macaque test input json * gzip fastqs * increase ulimit * rerun * rerun * rerun * rerun * changelogs * Updated pipeline_versions.txt with all pipeline version information * changelogs --------- Co-authored-by: GitHub Action <[email protected]> * point to new exome inputs * move inputs for now * Updated pipeline_versions.txt with all pipeline version information * move inputs for now * Updated pipeline_versions.txt with all pipeline version information * Updated pipeline_versions.txt with all pipeline version information * move inputs for now * new inputs * new inputs * Updated pipeline_versions.txt with all pipeline version information * Jw ao u filterand qc variants (#1589) * Add filter and QC WDL and python script --------- Co-authored-by: GitHub Action <[email protected]> * dummy commit * PD-2997: Add tests for Slide-Tags pipeline (#1585) * test * test * Updated pipeline_versions.txt with all pipeline version information * test * test * test * test * test * test * test * fix * test * Updated pipeline_versions.txt with all pipeline version information * test * Updated pipeline_versions.txt with all pipeline version information * test * test * test * test * test * json * Updated pipeline_versions.txt with all pipeline version information * json * add inputs for call to the verifySlideTags wdl * remove id input to slidetags * point the inputs to the private bucket for now just so we have access to run tests * add new task to compare stuff in tarballs * change name of verifytask alias * compare csvs using threshold logic * compare csvs using threshold logic * indentation * indentation * indentation * indentation * new threshold * col specific thresholds * new csv2 task * calculate tsse metrics only if fragment data is available * verbose * verbose * no thresholds for csv * change threshold for eps * change threshold for eps * change threshold for eps * increare more thresholds * fix compareh5file task * fix compareh5file task * exclude some columns from tests. * exclude some columns from tests. * exclude some columns from tests. * exclude some columns from tests. * exclude some columns from tests. * rewrite without tolerances * rewrite without tolerances * move out of beta * Updated pipeline_versions.txt with all pipeline version information * move out of beta * fix * fix * fix imports * Updated pipeline_versions.txt with all pipeline version information * add slidetags changelog first release * Updated pipeline_versions.txt with all pipeline version information * add slidetags changelog first release --------- Co-authored-by: GitHub Action <[email protected]> Co-authored-by: npetrill <[email protected]> Co-authored-by: Nikelle Petrillo <[email protected]> * fix input * update inputs * fix inputs * delete --------- Co-authored-by: aawdeh <[email protected]> Co-authored-by: Robert Sidney Cox <[email protected]> Co-authored-by: Farzaneh Khajouei <[email protected]> Co-authored-by: GitHub Action <[email protected]> Co-authored-by: Elizabeth Kiernan <[email protected]> Co-authored-by: Jessica Way <[email protected]>

aawdeh added 3 commits April 11, 2025 10:54

test

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Merge branch 'develop' of https://github.com/broadinstitute/warp into…

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… develop

added tar

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aawdeh changed the title ~~Aa slidetag~~ PD-2945: Update slide-tags Apr 11, 2025

modify

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modify

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modify

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modify

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fix

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Merge branch 'develop' into aa-slidetag

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aawdeh added 2 commits April 16, 2025 16:37

fix

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Merge branch 'aa-slidetag' of https://github.com/broadinstitute/warp …

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…into aa-slidetag

aawdeh added 2 commits April 16, 2025 16:39

fix

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fix

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documentation

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documentation

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Updated pipeline_versions.txt with all pipeline version information

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Merge branch 'develop' into aa-slidetag

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khajoue2 approved these changes Apr 23, 2025

View reviewed changes

nikellepetrillo approved these changes Apr 24, 2025

View reviewed changes

aawdeh merged commit ff3e3e0 into develop Apr 24, 2025
10 checks passed

aawdeh deleted the aa-slidetag branch April 24, 2025 13:20

PD-2945: Update slide-tags #1567

PD-2945: Update slide-tags #1567

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aawdeh commented Apr 11, 2025

Checklist

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