Search for a command to run...
[3.0.0] - 2026-02-23 Changed Set default pna_graph_component_size_min_threshold to 8000 instead of null (i.e. automatic) by @ptajvar #183. Removed Support for MPX in the pipeline by @johandahlberg #182 Enhancements & fixes Update schema files (e.g. explicitly use integer types for integers, rather than numbers) by @johandahlberg #184, #186 Add option to select custom containers for the experiment summary by @Aratz #186 Parameters | Old parameter | New parameter | | ---------------------------------------- | -------------------------------- | | | --experiment_summary_container | | --save_amplicon_reads | | | --trim_front | | | --trim_tail | | | --max_length | | | --min_length | | | --max_n_bases | | | --avg_qual | | | --dedup | | | --remove_polyg | | | --adapterqc_mismatches | | | --save_qc_passed_reads | | | --save_qc_failed_reads | | | --demux_mismatches | | | --demux_min_length | | | --save_demux_processed_reads | | | --save_demux_failed_reads | | | --markers_ignore | | | --algorithm | | | --max_neighbours | | | --collapse_mismatches | | | --collapse_min_count | | | --save_collapsed_reads | | | --multiplet_recovery | | | --graph_max_refinement_recursion_depth | | | --graph_max_edges_to_split | | | --graph_min_count | | | --save_edgelist | | | --min_size | | | --max_size | | | --dynamic_filter | | | --aggregate_calling | | | --save_raw_component_metrics | | | --save_annotate_dataset | | | --skip_analysis | | | --compute_polarization | | | --compute_colocalization | | | --use_full_bipartite | | | --polarization_transformation | | | --polarization_n_permutations | | | --polarization_min_marker_count | | | --colocalization_transformation | | | --colocalization_neighbourhood_size | | | --colocalization_n_permutations | | | --colocalization_min_region_count | | | --colocalization_min_marker_count | | | --save_analysis_dataset | | | --skip_layout | | | --no_node_marker_counts | | | --layout_algorithm | | | --skip_report | | [!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.