Gh pd 3055

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Based on the changes you've made, here's a pull request description for adding 10x 3' v4 (GEM-X) chemistry support to Optimus:

Pull Request Description
Description
Add 10x 3' v4 (GEM-X) chemistry support to Optimus pipeline

This PR adds support for 10x Genomics 3' v4 (GEM-X) chemistry to the Optimus pipeline while maintaining full backwards compatibility with existing v2 and v3 chemistries.

Changes Made
Added v4 chemistry support: New chemistry value 4 for 10x 3' v4 (GEM-X) chemistry
Enhanced whitelist selection: Added v4 whitelist paths for both GCP and Azure cloud providers
Updated chemistry validation: Extended existing validation logic to handle chemistry value 4
Maintained backwards compatibility: All existing v2/v3 workflows continue to work unchanged
Updated supporting tasks: Enhanced STARsolo, FastqProcessing, and Attach10xBarcodes tasks for v4 support
Motivation
The 10x 3' v4 (GEM-X) chemistry is the latest generation of single-cell RNA sequencing technology, offering improved performance and higher cell throughput. This PR enables users to process v4 data with Optimus while maintaining the same workflow structure and output formats they're familiar with from v2/v3 chemistries.

Technical Details
Chemistry value 4: Uses 16-bp cell barcodes + 12-bp UMIs (same read structure as v3)
Whitelist: Automatically selects 3M-3pgex-may-2023.txt.gz for v4 chemistry
STARsolo parameters: CB:1-16, UMI:17-28 for v4 chemistry
Read validation: Expects 28 bp R1 reads for v4 (same as v3)
Files Modified
pipelines/skylab/optimus/Optimus.wdl - Added v4 whitelist paths and chemistry support
tasks/skylab/CheckInputs.wdl - Extended chemistry validation for value 4
tasks/skylab/StarAlign.wdl - Enhanced STARsolo chemistry logic
tasks/skylab/FastqProcessing.wdl - Added v4 chemistry support
tasks/skylab/Attach10xBarcodes.wdl - Added v4 chemistry support
example_inputs/human_v4_example.json - New v4 chemistry example
Documentation files updated to reflect v4 support
Backwards Compatibility
✅ 100% backwards compatible: All existing v2/v3 workflows continue to work unchanged
✅ Same parameter structure: Uses existing Int chemistry parameter with new value 4
✅ No breaking changes: Existing JSON files and workflows require no modifications

Checklist
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?
@broadinstitute/warp-admins Added params for default v4 files (not yet available on our public references yet)

Link to the forked PR: #1664

[github-actions]

Remember to squash merge!

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
MultiSampleSmartSeq2SingleNucleus.changelog.md has not been changed and needs to be updated
PairedTag.changelog.md has not been changed and needs to be updated
SlideTags.changelog.md has not been changed and needs to be updated
atac.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
SlideSeq.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
MultiSampleSmartSeq2SingleNucleus.wdl has not been changed and needs updating
PairedTag.wdl has not been changed and needs updating
SlideTags.wdl has not been changed and needs updating
atac.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
SlideSeq.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed