nf-core/pixelator 4.1.2

[4.1.2] - 2026-06-04

Enhancements & fixes

• Update pixelator container to 0.28.0. This fixes a major performance regression in the graph step, which caused very high memory usage. By @johandahlberg #221

Software dependencies

Dependency	Old version	New version
pixelator	0.27.2	0.28.0

nf-core/pixelator 4.1.1

[4.1.1] - 2026-05-29

Enhancements & fixes

• Improve documentation by @Aratz #216
• Update pixelator by @Aratz #217

Software dependencies

Dependency	Old version	New version
pixelator	0.27.1	0.27.2

nf-core/pixelator 4.1.0

[4.1.0] - 2026-05-28

Enhancements & fixes

• Update pixelator container to 0.27.1 by @johandahlberg #212
• Denoise graph before sample calling step by @Aratz #212
• Add ACE and PLS denoising by @Aratz #212

Changed

• K1 denoising is turned off by default by @Aratz #212

Software dependencies

Dependency	Old version	New version
pixelator	0.26.0	0.27.1
pixelatorES	0.10.1	0.10.4

Parameters

Old parameter	New parameter
	--pna_denoise_run_ace_denoising
	--pna_denoise_ace_k
	--pna_denoise_run_pls_denoising
	--pna_denoise_pls_score_threshold

nf-core/pixelator 4.0.0

[4.0.0] - 2026-05-19

Added

• Add Proxiome V2 workflow support, enabling sample pooling and processing of up to 8,000 cells per run by @Aratz #204, #205

Enhancements & fixes

• Use nextflow strict syntax by @Aratz #194
• Use TMPDIR when defined to store temporary files by @Aratz #195
• Retry experiment summary up to two times after failure by @Aratz #196
• Updated pixelatorES to 0.10.1 in PNA experiment summary step by @Aratz #197, #204
• Add cells_1k and cells_8k Nextflow profiles with process-specific resource overrides for different input scales by @johandahlberg #203
• Fix singularity CI tests by @Aratz #208
• Update nf-core template to 4.0.2 by @Aratz #202

Software dependencies

Dependency	Old version	New version
pixelatorES	0.6.0	0.10.1
pixelator	0.23.0	0.26.0

Warning

Panel and design names have been completely renamed in pixelator 0.26 (nf-core/pixelator 4.0 and above). Refer to the pixelator changelog for more details.

Parameters

Old parameter	New parameter
--leiden-iterations
--min-component-size-in-refinement
--min-component-size-to-prune
	--edge_cycle-verification

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.

nf-core/pixelator 3.0.1

[3.0.1] - 2026-03-09

Enhancements & fixes

• Fix Issue #191 by @Aratz in #192

nf-core/pixelator 3.0.0

[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.

nf-core/pixelator 2.3.1

[2.3.1] - 2026-01-14

• Update usage documentation by @vincent-van-hoef #176
• Use PNA data in test profile by @Aratz #177

nf-core/pixelator 2.3.0

[2.3.0] - 2025-12-11

From this release onwards, there will not be a default panel selected, i.e. as a user you must specify an exact version of the panel you want to use in your samplesheet, e.g. proxiome-immuno-155-v2. The version to use will depend on which kit lot of the Proxiome Immuno kit you are using. See the Pixelgen Technologies website for an updated list of which panel version to use with which kit lot.

Removed

• Removed QC Report step from PNA pipeline (functionality is covered by the more extensive Experiment Summary step) by @johandahlberg #167

Enhancements & fixes

• Improve test suite by @Aratz #163
• Publish samplesheet to output directory by @Aratz #164
• Updated pixelatorES to 0.6.0 in PNA experiment summary step by @johandahlberg #168
• Updated pixelator to 0.23.0 in associated steps by @johandahlberg #168
• Give the collapse step more shared memory in the container to avoid out-of-memory errors by @stefanppetkov #169

Parameters

Old parameter	New parameter
	--pna_amplicon_low_complexity_filter
	--pna_amplicon_low_complexity_threshold
	--pna_amplicon_lbs_filter
	--pna_amplicon_lbs_filter_min_overlap
	--pna_amplicon_lbs_filter_error_rate

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	0.22.1	0.23.0
pixelatorES	0.4.3	0.6.0

nf-core/pixelator 2.2.0

[2.2.0] - 2025-11-05

This new minor version of nf-core/pixelator introduces new panel files with clearer names. These new
panels are now the default. To use the old version of the panels, append -v1 to the panel name in
the samplesheet, e.g. proxiome-immuno-155-v1.

Enhancements & fixes

• Update panel files with new names for marker ids by @Aratz #152
• New panel file with FLAG add-on by @Aratz #152
• Template update for nf-core/tools v3.4.1 by @Aratz in #151
• --input now accepts relative paths by @Aratz #153
• Pass down memory limits in PNA demux and combine-collapse by @fbdtemme #154
• Fix custom panel usage by @Aratz #156

Software dependencies

Dependency	Old version	New version
pixelator	0.21.4	0.22.1

nf-core/pixelator 2.1.0

[2.1.0] - 2025-09-17

Enhancements & fixes

• Move to using quay.io as the container source, to avoid issues with users needing to login to access the
  Github Container Registry by @johandahlberg in #140
• Add a denoise step to the PNA workflow, that cleans data between the graph and analysis steps
  by @johandahlberg in #140
• Fix the PNA report not being generated by @fbdtemme in #142
• Template update for nf-core/tools v3.3.2 by @fbdtemme in #143
• Add the experiment_summary step which generates the Proximity Experiment Summary report by @johandahlberg in #144
• Switch PIXELATOR_PNA_LAYOUT process label to process_high to allocate less memory by @ptajvar in #147
• Simplify PNA_GENERATE_REPORTS subworkflow by @fbdtemme in #150

Parameters

Old parameter	New parameter
	--skip_denoise
	--save_pna_denoise_pixelfile
	--pna_denoise_run_one_core_graph_denoising
	--pna_denoise_pval_threshold
	--pna_denoise_inflate_factor
	--pna_denoise_inflate_factor

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	0.20.1	0.21.4
pixelatorES		0.4.3

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.