nf-core/pixelator
Pipeline to generate Proximity Network Assay data with Pixelator (Pixelgen Technologies AB)
Version history
[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 |
[4.1.1] - 2026-05-29
Enhancements & fixes
Software dependencies
| Dependency | Old version | New version |
|---|---|---|
pixelator | 0.27.1 | 0.27.2 |
[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
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 |
[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
TMPDIRwhen 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_1kandcells_8kNextflow 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.
[3.0.1] - 2026-03-09
Enhancements & fixes
[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.
[2.3.1] - 2026-01-14
- Update usage documentation by @vincent-van-hoef #176
- Use PNA data in test profile by @Aratz #177
[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
collapsestep 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 |
[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
--inputnow 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 |
[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_summarystep 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.
This release is a major update of the nf-core/pixelator pipeline. It brings in support for the Proximity Network Analysis (PNA) workflow in addition to the Molecular Pixelation (MPX) workflow. Any run of the pipeline will now run the appropriate workflow depending on which design is specified in the input samplesheet.
What’s Changed
- Sync dev branch with master by @fbdtemme in https://github.com/nf-core/pixelator/pull/127
- Important! Template update for nf-core/tools v3.2.1 by @nf-core-bot in https://github.com/nf-core/pixelator/pull/132
- Update to pixelator 0.20.x by @johandahlberg in https://github.com/nf-core/pixelator/pull/131
- Update README to include information about PNA by @johandahlberg in https://github.com/nf-core/pixelator/pull/133
- Load missing pna modules by @johandahlberg in https://github.com/nf-core/pixelator/pull/135
- Prepare change log by @johandahlberg in https://github.com/nf-core/pixelator/pull/134
- Disable conda in CI tests by @fbdtemme in https://github.com/nf-core/pixelator/pull/136
- Bump version to 2.0.0 by @fbdtemme in https://github.com/nf-core/pixelator/pull/137
- Release pixelator 2.0 by @fbdtemme in https://github.com/nf-core/pixelator/pull/138
Full Changelog: https://github.com/nf-core/pixelator/compare/1.4.0…2.0.0
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_json | |
--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 | 0.20.1 |
[!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.
What’s Changed
- Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in https://github.com/nf-core/pixelator/pull/111
- Add graph refinement options for pixelator 0.19 by @fbdtemme in https://github.com/nf-core/pixelator/pull/112
- Fix validation issues after nf-core/tools v3 template update by @fbdtemme in https://github.com/nf-core/pixelator/pull/113
- Remove
--save_recovered_componentsoptions for graph outputs by @fbdtemme in https://github.com/nf-core/pixelator/pull/114 - Update containers for 0.19.0 by @fbdtemme in https://github.com/nf-core/pixelator/pull/115
- Bump version for 1.4 release by @fbdtemme in https://github.com/nf-core/pixelator/pull/116
- Important! Template update for nf-core/tools v3.1.0 by @nf-core-bot in https://github.com/nf-core/pixelator/pull/117
- Update metromap, bump conda versions by @fbdtemme in https://github.com/nf-core/pixelator/pull/118
- Add
process_longlabels to AMPLICON and COLLAPSE by @fbdtemme in https://github.com/nf-core/pixelator/pull/120 - Important! Template update for nf-core/tools v3.1.1 by @mirpedrol in https://github.com/nf-core/pixelator/pull/122
- Add manifest.contributors metadata to nextflow.config by @fbdtemme in https://github.com/nf-core/pixelator/pull/124
- Use environment.yml files for all conda process directives by @fbdtemme in https://github.com/nf-core/pixelator/pull/125
- Add nf-test tests for local modules and subworkflows by @fbdtemme in https://github.com/nf-core/pixelator/pull/123
- Release 1.4 by @fbdtemme in https://github.com/nf-core/pixelator/pull/121
Parameters
| Old parameter | New parameter |
|---|---|
--help_full | |
--show_hidden | |
--validationFailUnrecognisedParams | |
--validationLenientMode | |
--validationSchemaIgnoreParams | |
--validationShowHiddenParams | |
--leiden_iterations | --graph_max_refinement_recursion_depth |
--graph_max_edges_to_split | |
--graph_max_edges_to_split | |
--save_recovered_components |
[!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 | 0.18.2 | 0.19.0 |
[!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.
New Contributors
- @mirpedrol made their first contribution in https://github.com/nf-core/pixelator/pull/122
Full Changelog: https://github.com/nf-core/pixelator/compare/1.3.1…1.4.0
What’s Changed
- Fix conda version tag to use pixelator 0.18.2 by @fbdtemme in https://github.com/nf-core/pixelator/pull/107
- Patch release 1.3.1 by @fbdtemme in https://github.com/nf-core/pixelator/pull/108
Full Changelog: https://github.com/nf-core/pixelator/compare/1.3.0…1.3.1
What’s Changed
- chore: sync dev after release and bump to 1.3.0dev by @fbdtemme in https://github.com/nf-core/pixelator/pull/95
- Make
task.extassigments closures by @fbdtemme in https://github.com/nf-core/pixelator/pull/96 - Update metromap to include layout step by @fbdtemme in https://github.com/nf-core/pixelator/pull/98
- Update citations by @fbdtemme in https://github.com/nf-core/pixelator/pull/97
- Chore/update readme by @ambarrio in https://github.com/nf-core/pixelator/pull/99
- Use R1/R2 suffixes in amplicon input fastq file renaming by @fbdtemme in https://github.com/nf-core/pixelator/pull/100
- Fix validation issue when using panel_file instead of panel by @fbdtemme in https://github.com/nf-core/pixelator/pull/101
- Restructure output folder by @fbdtemme in https://github.com/nf-core/pixelator/pull/102
- Make rate diff default colocalization transformation by @johandahlberg in https://github.com/nf-core/pixelator/pull/103
- Update pixelator to 0.18.1 by @fbdtemme in https://github.com/nf-core/pixelator/pull/104
- Bump version to 1.3.0 by @fbdtemme in https://github.com/nf-core/pixelator/pull/105
- Release pixelator 1.3.0 by @fbdtemme in https://github.com/nf-core/pixelator/pull/106
New Contributors
- @ambarrio made their first contribution in https://github.com/nf-core/pixelator/pull/99
Software versions
Software dependencies
| Dependency | Old version | New version |
|---|---|---|
pixelator | 0.17.1 | 0.18.2 |
[!NOTE] Dependency has been updated if both old and new version information is present. Dependency has been added if just the new version information is present. Dependency has been removed if new version information isn’t present.
Full Changelog: https://github.com/nf-core/pixelator/compare/1.2.0…1.3.0
What’s Changed
- Template update for nf-core/tools v2.14.1 by @fbdtemme in https://github.com/nf-core/pixelator/pull/89
- Update pixelator to 0.17.1 by @johandahlberg in https://github.com/nf-core/pixelator/pull/90
- Set
process_highto use 64GB of RAM andprocess_high_memoryto use 128GB of RAM by @johandahlberg in https://github.com/nf-core/pixelator/pull/91 - Minor documentation fixes by @johandahlberg in https://github.com/nf-core/pixelator/pull/92
- Improve read renaming by @fbdtemme in https://github.com/nf-core/pixelator/pull/93
- Release nf-core/pixelator 1.2.0 by @fbdtemme in https://github.com/nf-core/pixelator/pull/94
Full Changelog: https://github.com/nf-core/pixelator/compare/1.1.0…1.2.0
What’s Changed
- Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in https://github.com/nf-core/pixelator/pull/83
- Update to pixelator 0.16.2 by @johandahlberg in https://github.com/nf-core/pixelator/pull/84
- Remove a workaround for container issues, silence some warnings, update default resources by @fbdtemme in https://github.com/nf-core/pixelator/pull/85
- Release pixelator 1.1.0 by @fbdtemme in https://github.com/nf-core/pixelator/pull/86, https://github.com/nf-core/pixelator/pull/87
Software dependencies
| Dependency | Old version | New version |
|---|---|---|
pixelator | 0.15.2 | 0.16.2 |
NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if new version information isn’t present.
Full Changelog: https://github.com/nf-core/pixelator/compare/1.0.3…1.1.0
What’s Changed
- Important! Template update for nf-core/tools v2.11 by @nf-core-bot in https://github.com/nf-core/pixelator/pull/74
- fix: use adapterqc output as main output of PIXELATOR_QC by @fbdtemme in https://github.com/nf-core/pixelator/pull/76
- fix validation issues with meta-schema by @fbdtemme in https://github.com/nf-core/pixelator/pull/77
- Prepare release 1.0.3 by @fbdtemme in https://github.com/nf-core/pixelator/pull/78
- Release 1.0.3 by @fbdtemme in https://github.com/nf-core/pixelator/pull/79
New Contributors
- @nf-core-bot made their first contribution in https://github.com/nf-core/pixelator/pull/74
Full Changelog: https://github.com/nf-core/pixelator/compare/1.0.2…1.0.3
[1.0.1] - 2023-10-27
Enhancements & fixes
- [PR #66] - Add a warning and workaround for singularity & apptainer
- Cleanup some linting warnings
- Update docker image in RENAME_READS to match the singularity container
Software dependencies
| Dependency | Old version | New version |
|---|---|---|
pixelator | 0.15.0 | 0.15.2 |
NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if new version information isn’t present.
[1.0.0] - 2023-10-17
Initial release of nf-core/pixelator.