Fk build indices marmoset

[khajoue2]

Description

Enhance GTF processing for Marmoset organism in RNA pipeline

This PR improves the handling of mitochondrial genes in Marmoset GTF files by introducing organism-specific processing steps. The changes ensure proper annotation and formatting of mitochondrial gene entries while maintaining compatibility with the existing GTF modification pipeline.

Key changes:

1. Added conditional GTF processing specific to Marmoset organism
2. Enhanced GTF attribute handling to ensure gene_name attributes are present
3. Implemented special processing for chrM entries in Marmoset GTFs
4. Maintained backwards compatibility with existing GTF processing for other organisms

Motivation:
The existing GTF processing pipeline did not adequately handle Marmoset-specific mitochondrial gene annotations. This change addresses the need for proper formatting and annotation of mitochondrial genes in Marmoset GTFs while ensuring the rest of the GTF processing remains intact.

Checklist

• Did you add inputs, outputs, or tasks to a workflow?
  • Added new organism-specific conditional processing to existing task

@broadinstitute/warp-admins Please review these changes to the GTF processing workflow.

[github-actions]

Remember to squash merge!

[github-actions]

🔍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]

🔍Changelog Validation Results:

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