[Aratz]

[5.0.0] - 2026-07-13

Changed

• (breaking change) Rename pna_sample_calling_confidence_threshold to pna_sample_calling_enrichment_threshold to match pixelator 0.29.0. By @elhb #227
• Change default layout algorithm from wpmds_3d to coarsened_pmds_3d. By @elhb #227
• Change pna_graph_refinement_stage_leiden_resolution and pna_graph_refinement_stage_max_edges_to_remove default values to 0.5, and 20 respectively based on latest evaluations. By @ptajvar #226
• Set pna_sample_calling_save_undetermined by default and deliver the undetermined PXL file at the pixelator/ output root, next to the final (layout) PXL files. By @Aratz #229

Enhancements & fixes

• Update pixelator container to 0.29.0
• Update pixelatorES to 0.11.2

Software dependencies

Dependency	Old version	New version
pixelator	0.28.0	0.29.0
pixelatorES	0.10.4	0.11.2

Parameters

Old parameter	New parameter
pna_sample_calling_confidence_threshold	pna_sample_calling_enrichment_threshold

Note

Parameter has been updated if both old and new parameter information is present.
Parameter has been added if just the new parameter information is present.
Parameter has been removed if new parameter information isn't present.