Ronghao eRZ59 Split 4m novaseq

[ShanshanHe-44]

Changes

1) Default results directory

• Add a self-default results directory to store analysis outputs when --results_dir/RESULTS is not explicitly provided.

2) Species support: mouse + reference paths

• Introduce a species parameter supporting human and mouse.
• Add corresponding mouse reference paths (and select reference automatically based on species), ensuring consistent mapping/annotation behavior across species.

3) Gene annotation updates (mouse + mitochondrial)

• Update gene annotation to align with the future mouse reference (ref name/version as configured in the pipeline).
• Improve mitochondrial gene handling for mouse (e.g., mt- prefix / MT detection logic), and ensure mitochondrial QC fields are correctly populated for downstream metrics.

4) Cell calling updates + barcode rank plots

• Perform cell calling per bio sample (bio-sample–level calling) to better reflect experimental grouping and reduce mixing artifacts.
• Add output plots from utility functions for droplet cell barcode rank (barcode rank / knee-plot style), and include them in the cell calling output folder for QC reporting.