Skip to content

CHANGELOG.md

Latest commit

 

History

History
527 lines (405 loc) · 29.6 KB

CHANGELOG.md

File metadata and controls

527 lines (405 loc) · 29.6 KB

nf-core/pixelator: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[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

[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

[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
--technology
--edge_cycle-verification
save_pna_sample_calling_pixelfile
pna_sample_calling_save_undetermined
pna_sample_calling_remove_incompatible
pna_sample_calling_confidence_threshold

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

  • Fix Issue #191 by @Aratz #192

[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 collapse step more shared memory in the container to avoid out-of-memory errors by @stefanppetkov #169
  • Update nf-core template to 3.5.1 by @Aratz #165

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] - 2025-11-02

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

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.

[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.

[2.0.0] - 2024-05-27

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.

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_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.

[1.4.0] - 2024-01-22

Enhancements & fixes

  • [PR #111] - Template update for nf-core/tools v3.0.2
  • [PR #112] - Add graph refinement options for pixelator 0.19
  • [PR #113] - Fix validation issues after nf-core/tools v3.0.2 update
  • [PR #114] - Remove --save_recovered_components options for graph outputs
  • [PR #115] - Update containers for pixelator 0.19
  • [PR #116] - Bump version to 1.4
  • [PR #117] - Template update for nf-core/tools v3.1.0
  • [PR #118] - Update metromap, bump conda versions
  • [PR #120] - Add process_long to AMPLICON and COLLAPSE steps
  • [PR #122] - Template update for nf-core/tools v3.1.1
  • [PR #124] - Add manifest.contributors metadata to nextflow.config
  • [PR #125] - Use environment.yml files for all conda process directives
  • [PR #123] - Add nf-test tests for local modules and subworkflows

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.

[1.3.1] - 2024-07-31

Enhancements & fixes

  • [PR #107] - Fix conda version tag to use pixelator 0.18.2

[1.3.0] - 2024-07-17

Enhancements & fixes

  • [PR #97] - Update citations
  • [PR #96] - Make all ext.args assignments closures
  • [PR #98] - Update metromap to include layout step
  • [PR #99] - Update README to include layout step
  • [PR #100] - Use R1/R2 suffixes in amplicon input fastq file renaming
  • [PR #101] - Fix validation issue when using panel_file instead of panel
  • [PR #102] - Restructure output directory
  • [PR #103] - Make rate-diff the default transformation method when computing colocalization
  • [PR #104] - Update to pixelator 0.18.1
  • [PR #106] - Update to pixelator 0.18.2

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.

[1.2.0] - 2024-05-28

Enhancements & fixes

  • [PR #89] - Template update for nf-core/tools v2.14.1
  • [PR #90] - Update pixelator to 0.17.1
  • [PR #90] - Add pixelator single-cell layout command
  • [PR #90] - The graph and annotate steps are now using process_high as their resource tags
  • [PR #91] - Set process_high to use 64GB of RAM and process_high_memory to use 128GB of RAM
  • [PR #92] - Minor touch-ups to the documentation
  • [PR #93] - Merge RENAME_READS functionality into PIXELATOR_AMPLICON

Software dependencies

Dependency Old version New version
pixelator 0.16.2 0.17.1

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.

[1.1.0] - 2024-03-29

Enhancements & fixes

  • [PR #83] - Template update for nf-core/tools v2.13
  • [PR #84] - Update pixelator to 0.16.2, collapseandgraph` step now return parquet files
  • [PR #85] - Remove a workaround for container issues, silence some warnings, update default resources

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.

[1.0.3] - 2024-01-19

Enhancements & fixes

  • [PR #74] - Template update for nf-core/tools v2.11
  • [e196431] - Workaround a tool issue by removing docker.runOptions user and group flags
  • [PR #76] - Use adapterqc output as main output of PIXELATOR_QC
  • [PR #77] - Fix some style issues in nextflow_schema.json

[1.0.2] - 2023-11-20

Enhancements & fixes

  • [PR #70] - Fix loading of absolute paths and urls in input samplesheet

[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.