updates for tenx v4 chemistry

[gileshall]

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

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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)