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staging --> master #1484

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ekiernan
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staging --> master

nikellepetrillo and others added 14 commits December 10, 2024 21:14
@nikellepetrillo @actions-user
add cellbender to optimus (#1446)
2fffa87 
* add cellbender to optimus

* changelogs

* Updated pipeline_versions.txt with all pipeline version information

* changelogs

* try cellbender is true

* try cellbender is true

* extra slash

---------

Co-authored-by: GitHub Action <[email protected]>
@nikellepetrillo
add beta test optimus.yml (#1459)
f55ea75 
* add beta test optimus.yml

* add beta test optimus.yml

* add beta test optimus.yml
@nikellepetrillo
Delete .github/workflows/beta_test_optimus.yml
642e3f2
@jessicaway @actions-user
Update output names for ReblockGVCF (#1443)
6e9963c 
* Update output names for ReblockGVCF

---------

Co-authored-by: GitHub Action <[email protected]>
@dependabot @nikellepetrillo
Bump braces from 3.0.2 to 3.0.3 in /website (#1427)
c9135b7 
Bumps [braces](https://github.com/micromatch/braces) from 3.0.2 to 3.0.3.
- [Changelog](https://github.com/micromatch/braces/blob/master/CHANGELOG.md)
- [Commits](micromatch/braces@3.0.2...3.0.3)

---
updated-dependencies:
- dependency-name: braces
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Nikelle Petrillo <[email protected]>
@dependabot @nikellepetrillo
Bump cross-spawn from 7.0.3 to 7.0.6 in /website (#1430)
46439be 
Bumps [cross-spawn](https://github.com/moxystudio/node-cross-spawn) from 7.0.3 to 7.0.6.
- [Changelog](https://github.com/moxystudio/node-cross-spawn/blob/master/CHANGELOG.md)
- [Commits](moxystudio/node-cross-spawn@v7.0.3...v7.0.6)

---
updated-dependencies:
- dependency-name: cross-spawn
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Nikelle Petrillo <[email protected]>
@dependabot @nikellepetrillo
Bump nanoid from 3.3.6 to 3.3.8 in /website (#1449)
fb58fe4 
Bumps [nanoid](https://github.com/ai/nanoid) from 3.3.6 to 3.3.8.
- [Release notes](https://github.com/ai/nanoid/releases)
- [Changelog](https://github.com/ai/nanoid/blob/main/CHANGELOG.md)
- [Commits](ai/nanoid@3.3.6...3.3.8)

---
updated-dependencies:
- dependency-name: nanoid
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Nikelle Petrillo <[email protected]>
@dependabot @nikellepetrillo
Bump jinja2 from 3.1.4 to 3.1.5 in /verification/test-wdls/scripts (#…
35675f7 
…1454)

Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.4 to 3.1.5.
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst)
- [Commits](pallets/jinja@3.1.4...3.1.5)

---
updated-dependencies:
- dependency-name: jinja2
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Nikelle Petrillo <[email protected]>
@rsc3
add pairedtag diagram and fix snm3c slug (#1469)
a7b1952 
* add pairedtag diagram and fix snm3c slug

* add pairedtag diagram and fix snm3c slug

* move pairedtag diagram below version box
@aawdeh
PD-2757: Add Optimus as first task to the Slidetag WDL (#1440)
a4f334b
@ekiernan
Lk pd 2814 adding gtf h5ad (#1470)
cde33b7 
added the path for reference GTF file to Multiome h5ad outputs
@ekiernan
Lk pd 2836 marmoset (#1480)
256b324 
Updated BuildIndices to include docker with Marmoset scripts for modifying custom marmoset reference
@ekiernan
adding Paired-tag EM multimapping and csi index output (#1482)
eedabad 
added EM multimapping and csi index output to PairedTag WDL
@ekiernan
Merge pull request #1483 from broadinstitute/develop
5f54699 
dev --> staging
@github-actions GitHub Actions
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DO NOT SQUASH MERGE!!!

@github-actions GitHub Actions
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🔍Changelog Validation Results:

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

@github-actions GitHub Actions
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🔍Version Validation Results:

basename: missing operand
Try 'basename --help' for more information.
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.

@ekiernan
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retest this please

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5 participants
@ekiernan @nikellepetrillo @jessicaway @rsc3 @aawdeh