V2 Pipeline Implementation (Part 3)

[btmonier]

Summary

Extends the v2 orchestrate pipeline with the final four steps (highlighted below). Also refactors orchestrator step banners into a shared logBanner() helper used by both v1 and v2.

Features

• Add v2 orchestrate steps:
  • convert_to_fasta
  • build_spline_knots
  • RopeBWT3 index and aligner wrapper
  • convert_ropebwt2ps4g
• Add necessary FASTQ input to YAML
• Updates to example docs
• Refactor orchestrator logging banners into shared OrchestrateShared.logBanner() (used by OrchestrateV1 and OrchestrateV2)

Bug Fixes

• None

Breaking Changes

• None

Checklist

• I have updated the version in build.gradle.kts (REQUIRED - see below)
• I have tested these changes locally
• I have added/updated tests for new functionality
• I have updated documentation (if applicable)
• Breaking changes are clearly documented above (if applicable)