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Rc 3220 scvi scanvi pipeline#1766

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rsc3 wants to merge 37 commits intodevelopfrom
rc_3220_scvi
Closed

Rc 3220 scvi scanvi pipeline#1766
rsc3 wants to merge 37 commits intodevelopfrom
rc_3220_scvi

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@rsc3 rsc3 commented Feb 9, 2026

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?

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github-actions bot commented Feb 9, 2026

Remember to squash merge!

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github-actions bot commented Feb 9, 2026

🔍Changelog Validation Results:

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

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github-actions bot commented Feb 9, 2026

🔍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.

@rsc3 rsc3 marked this pull request as draft February 10, 2026 18:56
nikellepetrillo and others added 7 commits February 11, 2026 10:47
* dummy commit

* change logic of mito_Accession

* change logic of mito_Accession

* change logic of mito_Accession

* changelogs

* Updated pipeline_versions.txt with all pipeline version information

---------

Co-authored-by: GitHub Action <action@github.com>
update tests to work with new outputs
update documentation around pipeline

Co-authored-by: Jose Soto <jsoto@broadinstitute.org>
* add whitelist references to optimus

* Update website/docs/Pipelines/Optimus_Pipeline/README.md

Co-authored-by: Elizabeth Kiernan <55763654+ekiernan@users.noreply.github.com>

---------

Co-authored-by: Elizabeth Kiernan <55763654+ekiernan@users.noreply.github.com>
* add whitelist references to optimus

* refactor mitofinder business logic for buildindices workflow

* fix None literal

* buildincides flow reformat

* update changelog and optional parameter comments

* Updated pipeline_versions.txt with all pipeline version information

* buildindices refactor, updated metadata.txt for tasks

* Updated pipeline_versions.txt with all pipeline version information

* make biotypes.tsv optional

* test suite and update buildindices refactor with FixGeneNames

* Updated pipeline_versions.txt with all pipeline version information

* separate ValidateGTF and testing

* Updated pipeline_versions.txt with all pipeline version information

* changelog

* changelog

---------

Co-authored-by: GitHub Action <action@github.com>
Added initial scripts for subsettings VCFs for downstream analysis with FLARE for local ancestry
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Remember to squash merge!

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🔍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
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Copy Markdown

🔍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
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Remember to squash merge!

@github-actions
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🔍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
Copy link
Copy Markdown

🔍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
Copy link
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Remember to squash merge!

@github-actions
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🔍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
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Copy Markdown

🔍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
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Remember to squash merge!

@github-actions
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🔍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
Copy link
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🔍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
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github-actions bot commented Mar 9, 2026

Remember to squash merge!

@github-actions
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github-actions bot commented Mar 9, 2026

🔍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
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github-actions bot commented Mar 9, 2026

🔍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
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github-actions bot commented Mar 9, 2026

Remember to squash merge!

@github-actions
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github-actions bot commented Mar 9, 2026

🔍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
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github-actions bot commented Mar 9, 2026

🔍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
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github-actions bot commented Mar 9, 2026

Remember to squash merge!

@github-actions
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github-actions bot commented Mar 9, 2026

🔍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
Copy link
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github-actions bot commented Mar 9, 2026

🔍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
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github-actions bot commented Mar 9, 2026

Remember to squash merge!

@github-actions
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github-actions bot commented Mar 9, 2026

🔍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
Copy link
Copy Markdown

github-actions bot commented Mar 9, 2026

🔍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
Copy link
Copy Markdown

github-actions bot commented Mar 9, 2026

Remember to squash merge!

@github-actions
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github-actions bot commented Mar 9, 2026

🔍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
Copy link
Copy Markdown

github-actions bot commented Mar 9, 2026

🔍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
Copy link
Copy Markdown

github-actions bot commented Mar 9, 2026

Remember to squash merge!

@github-actions
Copy link
Copy Markdown

github-actions bot commented Mar 9, 2026

🔍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
Copy link
Copy Markdown

github-actions bot commented Mar 9, 2026

🔍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
Copy link
Copy Markdown

Remember to squash merge!

@github-actions
Copy link
Copy Markdown

🔍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
Copy link
Copy Markdown

🔍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.

@rsc3 rsc3 closed this Apr 14, 2026
@rsc3 rsc3 deleted the rc_3220_scvi branch April 14, 2026 18:39
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5 participants