nf-core/pixelator
Pipeline to generate Molecular Pixelation data with Pixelator (Pixelgen Technologies AB)
Version history
[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.
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