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Cell Ranger Multi Input (Smoke Pipeline)

This tool parses Cell Ranger multi configs and runs the feature-barcode pipeline to produce 10x-style MEX outputs suitable for early STAR Suite parity testing.

Usage

python3 tools/cr_multi/cr_multi.py \
  --multi-config /path/to/multi_config.csv \
  --feature-ref /path/to/feature_reference.csv \
  --whitelist /path/to/whitelist.txt \
  --assign-barcodes core/features/process_features/assignBarcodes \
  --mex-stub tools/feature_barcodes/assignbarcodes_mex_stub.py \
  --gex-mex /path/to/gex_mex_dir \
  --gex-filter-type "Gene Expression" \
  --outdir /path/to/output

The script expects the gex-mex directory to contain matrix.mtx(.gz), barcodes.tsv(.gz), and features.tsv(.gz).

Notes

  • This is a smoke-path implementation for feature MEX integration.
  • GEX processing via STAR is still separate; provide GEX MEX from STAR outputs when ready.