Release 5.0.0 by Aratz · Pull Request #231 · nf-core/pixelator

Aratz · 2026-07-13T07:30:11Z

[5.0.0] - 2026-07-13

Changed

(breaking change) Rename pna_sample_calling_confidence_threshold to pna_sample_calling_enrichment_threshold to match pixelator 0.29.0. By @elhb #227
Change default layout algorithm from wpmds_3d to coarsened_pmds_3d. By @elhb #227
Change pna_graph_refinement_stage_leiden_resolution and pna_graph_refinement_stage_max_edges_to_remove default values
to 0.5, and 20 respectively based on latest evaluations. By @ptajvar #226
Expose pna_graph_component_size_max_threshold. By @Aratz #233

Enhancements & fixes

Update pixelator container to 0.29.0. By @elhb #227
Update pixelatorES to 0.11.2. By @elhb #227
Condense ES script. By @Aratz #232

Software dependencies

Dependency	Old version	New version
`pixelator`	0.28.0	0.29.0
`pixelatorES`	0.10.4	0.11.2

Parameters

Old parameter	New parameter
`pna_sample_calling_confidence_threshold`	`pna_sample_calling_enrichment_threshold`
	`pna_graph_component_size_max_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.

Post release 4.1.2

…inement_stage_max_edges_to_remove default values

…pdated data

…r than moving)

…name

fix: reference test-datasets by commit sha rather than branch name

…parameters update pna_graph_refinement_stage_leiden_resolution and pna_graph_ref…

Save undetermined files by default

Pre release 5.0.0

github-actions · 2026-07-13T07:31:47Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 97c7107

+| ✅ 233 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   1 tests had warnings |!

Details

❗ Test warnings:

pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/pixelator/pixelator/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
_

❔ Tests ignored:

files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: tests/default.nf.test
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-pixelator_logo_light.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
multiqc_config - multiqc_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-pixelator_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/CONTRIBUTING.md
files_exist - File found: docs/images/nf-core-pixelator_logo_light.png
files_exist - File found: docs/images/nf-core-pixelator_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: main.nf
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-pixelator_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowPixelator.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version does not contain dev for release: 5.0.0
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.pna_amplicon_mismatches= 0.1
nextflow_config - Config default value correct: params.pna_amplicon_remove_polyg= true
nextflow_config - Config default value correct: params.pna_amplicon_quality_cutoff= 20
nextflow_config - Config default value correct: params.pna_amplicon_low_complexity_filter= true
nextflow_config - Config default value correct: params.pna_amplicon_low_complexity_threshold= 0.8
nextflow_config - Config default value correct: params.pna_amplicon_lbs_filter= true
nextflow_config - Config default value correct: params.pna_amplicon_lbs_filter_min_overlap= 8
nextflow_config - Config default value correct: params.pna_amplicon_lbs_filter_error_rate= 0.1
nextflow_config - Config default value correct: params.pna_demux_mismatches= 1
nextflow_config - Config default value correct: params.pna_demux_output_chunk_reads= 50M
nextflow_config - Config default value correct: params.pna_demux_output_max_chunks= 8
nextflow_config - Config default value correct: params.pna_demux_strategy= independent
nextflow_config - Config default value correct: params.pna_collapse_algorithm= directional
nextflow_config - Config default value correct: params.pna_collapse_mismatches= 2
nextflow_config - Config default value correct: params.pna_graph_multiplet_recovery= true
nextflow_config - Config default value correct: params.pna_graph_initial_stage_leiden_resolution= 1.0
nextflow_config - Config default value correct: params.pna_graph_refinement_stage_leiden_resolution= 0.5
nextflow_config - Config default value correct: params.pna_graph_edge_cycle_verification= true
nextflow_config - Config default value correct: params.pna_graph_min_count= 1.0
nextflow_config - Config default value correct: params.pna_graph_max_refinement_recursion_depth= 3
nextflow_config - Config default value correct: params.pna_graph_initial_stage_max_edges_to_remove= 10
nextflow_config - Config default value correct: params.pna_graph_refinement_stage_max_edges_to_remove= 20
nextflow_config - Config default value correct: params.pna_graph_component_size_min_threshold= 8000
nextflow_config - Config default value correct: params.pna_graph_component_size_max_threshold= 500000
nextflow_config - Config default value correct: params.pna_sample_calling_remove_incompatible= true
nextflow_config - Config default value correct: params.pna_sample_calling_enrichment_threshold= 10.0
nextflow_config - Config default value correct: params.pna_denoise_pval_threshold= 0.05
nextflow_config - Config default value correct: params.pna_denoise_inflate_factor= 1.5
nextflow_config - Config default value correct: params.pna_denoise_run_ace_denoising= true
nextflow_config - Config default value correct: params.pna_denoise_ace_k= 3
nextflow_config - Config default value correct: params.pna_denoise_run_pls_denoising= true
nextflow_config - Config default value correct: params.pna_denoise_pls_score_threshold= -3.0
nextflow_config - Config default value correct: params.pna_analysis_compute_proximity= true
nextflow_config - Config default value correct: params.pna_analysis_compute_k_cores= true
nextflow_config - Config default value correct: params.pna_analysis_proximity_nbr_of_permutations= 100
nextflow_config - Config default value correct: params.pna_analysis_compute_svd_var_explained= true
nextflow_config - Config default value correct: params.pna_analysis_svd_nbr_of_pivots= 50
nextflow_config - Config default value correct: params.pna_layout_layout_algorithm= coarsened_pmds_3d
nextflow_config - Config default value correct: params.pna_layout_pmds_pivots= 50
nextflow_config - Config default value correct: params.pna_layout_wpmds_k= 5
nextflow_config - Config default value correct: params.save_json= true
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/e8950f260973a6778e2ff24988e12fd4474d60e1/
nextflow_config - Config default value correct: params.modules_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/
nf_test_content - 'tests/proxiome_v1.nf.test' contains outdir parameter
nf_test_content - 'tests/proxiome_v1.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v1.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v1.nf.test' contains outdir parameter
nf_test_content - 'tests/proxiome_v1.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v2.nf.test' contains outdir parameter
nf_test_content - 'tests/proxiome_v2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/proxiome_v2.nf.test' contains outdir parameter
nf_test_content - 'tests/proxiome_v2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/images/nf-core-pixelator_logo_light.png matches the template
files_unchanged - docs/images/nf-core-pixelator_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 25.10.4, Config: 25.10.4
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - PIXELATOR found in conf/modules.config and Nextflow scripts.
modules_config - PIXELATOR_LIST_OPTIONS found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 4.0.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 5.0.0, nfcore_yml.version = 5.0.0
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 4.0.2
Run at 2026-07-15 12:07:08

…ned" This reverts commit d1f9a45, reversing changes made to a2470e2.

Revert undetermined

Expose `pna_graph_component_size_max_threshold`

johandahlberg and others added 30 commits June 4, 2026 11:30

Bump version to 4.2.0dev

b3ffee2

Merge pull request #224 from nf-core/post-release-4.1.2

5050af7

Post release 4.1.2

update pna_graph_refinement_stage_leiden_resolution and pna_graph_ref…

29edc94

…inement_stage_max_edges_to_remove default values

update CHANGELOG.md

dbadda3

lower pna_graph_component_size_min_threshold for v2 test

234b741

lower pna_graph_component_size_min_threshold for v2 test to 2

873851e

set pna_graph_component_size_min_threshold to 10 for both v1 and v2

cdaec15

update to pixelator 0.29.0

17e0f0e

update default layout wpmds_3d -> coarsened_pmds_3d

3109c73

Empty commit to retrigger tests

c4c7089

update confidence threshold to the new enrichment threshold

ff5c27d

update to latest pixelatorES version

da36081

update tests to use the prerelease v2 panel

4cd4a45

fix: make test use the correct technology parameter i.e. proxiome-v2

c5f74ef

update a missed test to use the prerelease v2 panel

00ee092

update ES test, denoise now on pool level before sample calling

660d8ba

fall back to wpmds_3d when components in test data are too small

b9dfa13

fix pna_layout_layout_algorithm

fdbc9be

temporary change of test-data location to make sure tests pass with u…

40dc85f

…pdated data

update snaps

7fbe929

Merge branch 'dev' into update-to-pixelator-0.29.0

5b973d3

update changelog and output.md

f31b7a1

lint fix

a398397

set test pna_graph_component_size_min_threshold to 25

3ec7e58

point datasets to specific commit rather than branch (set point rathe…

8a9e5e4

…r than moving)

fix: point to commit sha on nf-core/test-datasets rather than branch …

2d0dc1b

…name

Merge pull request #228 from nf-core/lock-test-dataset-version

dcfa53a

fix: reference test-datasets by commit sha rather than branch name

update test data paths

417c561

Merge branch 'dev' into update-to-pixelator-0.29.0

6294d82

update commit sha

feeaa9d

Aratz added 13 commits June 22, 2026 16:19

Merge pull request #226 from nf-core/update-graph-refinement-default-…

a2470e2

…parameters update pna_graph_refinement_stage_leiden_resolution and pna_graph_ref…

Save undetermined cells by default

cefd572

Condense ES debug output

a0de6b9

Update Changelog

d633901

Update missing snapshots

d326ca2

Set save_pna_sample_calling_pixelfile on by default

e1fd7e8

Revert save_pna_sample_calling_pixelfile to false by default

14d2492

Publish undetermined in root output

1d59754

Merge pull request #229 from Aratz/pna-2844/default_undetermined

d1f9a45

Save undetermined files by default

Clean-up changelog

9f71b4e

Bump version to 5.0.0

28601cd

Load custom config

1b43d45

Merge pull request #230 from Aratz/pre-release_5.0.0

80b7c1e

Pre release 5.0.0

Aratz requested review from johandahlberg and ptajvar July 13, 2026 07:30

Aratz requested a review from a team as a code owner July 13, 2026 07:30

ptajvar approved these changes Jul 13, 2026

View reviewed changes

johandahlberg approved these changes Jul 13, 2026

View reviewed changes

Aratz added 9 commits July 15, 2026 08:31

Add missing changelog attributions

15c7aad

Fix typo

3270108

Revert "Merge pull request #229 from Aratz/pna-2844/default_undetermi…

19a207a

…ned" This reverts commit d1f9a45, reversing changes made to a2470e2.

Condense ES debug output

5a263af

Update changelog

3941a11

Clean up obsolete snapshot

9281070

Merge pull request #232 from Aratz/revert_undetermined

ca3d64d

Revert undetermined

Expose pna_graph_component_size_max_threshold

1d3f36e

Merge pull request #233 from Aratz/feature/expose_max_component_size

97c7107

Expose `pna_graph_component_size_max_threshold`

Aratz self-assigned this Jul 16, 2026

Aratz merged commit 5a75705 into master Jul 16, 2026
37 checks passed

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Release 5.0.0 - #231

Release 5.0.0#231
Aratz merged 57 commits into
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Aratz commented Jul 13, 2026 •

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Aratz commented Jul 13, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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[5.0.0] - 2026-07-13

Changed

Enhancements & fixes

Software dependencies

Parameters

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github-actions Bot commented Jul 13, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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Aratz commented Jul 13, 2026 •

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️