- Removed the Zarr formatted matrix and metrics outputs and replaced with Loom
- Removed EmptyDrops for sn_rna mode
- Updated the Loom file attribute names: CellID to cell_names, Gene to gene_names, and Accession to ensembl_ids
- Added metrics for mitochondrial reads
- Added an optional input for the BAM basename; this input is listed as ‘bam_output_basename’ and the default is 'sample_id'