Release pixelator 2.0

[fbdtemme]

Release nf-core/core pixelator v2

[2.0.0] - 2025-06-23

This release is a major update of the nf-core/pixelator pipeline. It brings in support for the
Proximity Network Analysis (PNA) workflow. Any run of the pipeline will now run the appropriate
workflow depending on which design is specified in the input samplesheet.

Enhancements & fixes

• [PR #131] - Update to pixelator 0.20.1, and add PNA workflows
• [PR #132] - Template update for nf-core/tools v3.2.1
• [PR #133] - Documentation updates

Parameters

Old parameter	New parameter
	--save_pna_demux_parquet
	--save_pna_demux_passed_reads
	--save_pna_demux_failed_reads
	--save_pna_collapsed_reads
	--save_pna_graph_pixelfile
	--save_pna_analysis_pixelfile
	--save_pna_all
	--pna_amplicon_mismatches
	--pna_amplicon_remove_polyg
	--pna_amplicon_quality_cutoff
	--pna_demux_mismatches
	--pna_demux_output_chunk_reads
	--pna_demux_output_max_chunks
	--pna_demux_strategy
	--pna_collapse_mismatches
	--pna_collapse_algorithm
	--pna_graph_multiplet_recovery
	--pna_graph_leiden_iterations
	--pna_graph_initial_stage_leiden_resolution
	--pna_graph_refinement_stage_leiden_resolution
	--pna_graph_min_count
	--pna_graph_min_component_size_in_refinement
	--pna_graph_max_refinement_recursion_depth
	--pna_graph_initial_stage_max_edges_to_remove
	--pna_graph_refinement_stage_max_edges_to_remove
	--pna_graph_initial_stage_max_edges_to_remove_relative
	--pna_graph_refinement_stage_max_edges_to_remove_relative
	--pna_graph_graph_min_component_size_to_prune
	--pna_graph_component_size_min_threshold
	--pna_analysis_compute_proximity
	--pna_analysis_proximity_nbr_of_permutations
	--pna_analysis_compute_k_cores
	--pna_analysis_compute_svd_var_explained
	--pna_analysis_svd_nbr_of_pivots
	--pna_layout_no_node_marker_counts
	--pna_layout_layout_algorithm
	--pna_layout_pmds_pivots
	--pna_layout_wpmds_k

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.

Software dependencies

Dependency	Old version	New version
pixelator	0.19.0	0.21.1

Note

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

[maxulysse]

Just a quick first pass from my side, but:
I agree with James comments
I would keep MultiQC even if just to display versions.
Minor comments from @yuukiiwa still need to be addressed.

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[fbdtemme]

I don't know if this is been raised before, but is there a reason for all the local modules despite pixelator being consistent used/seemed to be it's own package (so presumably it's a solid bit of software)?

It would make release PRs much easier if the modules have already been reviewed by otheres in nf-core/modules.

The reason they have not been upstreamed yet is because use of these tools outside of the pipeline has limited use. So for Pixelgen it is more convenient to have that in a single repo. But I follow the ease of review argument and we will discuss furher internally.

[fbdtemme]

We removed multiqc since we are indeed only using it for version reporting and the pixelator report already includes the versions. Since there is no other tools used (except cat) we felt that it would be too redundant.

We run the template with multiqc feature disabled so the methods_description_template.yml is already removed from the template branch. We needed to delete it here again because due to a previous bad sync from the template bringing that in again.

Would like it be ok to bring MultiQC back with the next release instead of doing that now?

[fbdtemme]

Thanks for your reviews @yuukiiwa @maxulysse @jfy133!
It took a while for me to get to adressing the comments but I think all should be fixed or the reasons clarified. Could you have a look again?

[maxulysse]

We removed multiqc since we are indeed only using it for version reporting and the pixelator report already includes the versions. Since there is no other tools used (except cat) we felt that it would be too redundant.

We run the template with multiqc feature disabled so the methods_description_template.yml is already removed from the template branch. We needed to delete it here again because due to a previous bad sync from the template bringing that in again.

Would like it be ok to bring MultiQC back with the next release instead of doing that now?

OK for me in such a case

[jfy133]

Most of my comments were addressed, although one I think slipt through (despite a commit to keep it).

I agree with re-adding MultiQC on the next release to not block this one to keep in line with template etc, even if your own report is primary report (which is fine).