25-258

First public release.
This version introduces major structural updates, improved performance, and clearer input handling.

🚀 New

• New step: CONCAT_FASTQS
  Collapses lane-split FASTQs into single R1/R2 files per sample.
  • Skips samples that already have a single pair.
  • Standardizes naming for clean downstream matching.

✨ Improvements

• Inputs & Groups
  • Restructured input style: added clearer group ID handling in sample maps.
  • Whitelist CSV is now stored directly in the repository.
• FIND_LARRY_SEQS
  • Underlying CBUtools and Dockerfile changes enable parallelisation, yielding >4× faster runtime.
• LARRY_QC
  • Added more logging between filters for transparency.
  • Fixed QC plots and text in the PDF report.
  • Whitelist directory now defaults to the repo path.
• ASSIGN_BARCODES (formerly ASSIGN_CLONES)
  • Renamed for clarity and consistency with the poster/README.
  • Refactored to support the new input structure.
  • Removed combine_samples functionality (now handled via group IDs).
• MATCH_GEX
  • Added support for Cell Ranger outputs (in addition to STARsolo).
  • Refactored to support the new input structure.

🛠 Internal

• Updated Dockerfile: streamlined how CBUtools is installed and used.
• Modified process resources and updated Singularity image.
• Cleaned up example files/scripts.
• Removed old git submodule.