openpipelines.bio v4.1.1

BUG FIXES

• annotate/scanvi: no longer predicts cell type labels that are absent from the reference. Reference label columns often declare more categories than are actually used (e.g. when the reference is a subset of a larger atlas), which previously caused scANVI to occasionally assign query cells to those empty labels. Unused labels are now dropped before training (PR #1207).

• workflows/prot/prot_multisample: Fix passing arguments --output_var_num_nonzero_obs and --output_var_pct_dropout arguments to qc workflow (PR #1196).