Release 4.0.0 by Aratz · Pull Request #207 · nf-core/pixelator

Aratz · 2026-05-19T11:33:32Z

[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.

Bump version to 3.1.0dev

Merge changes from patch 3.0.1 back into dev

As far as I understand, this was set so that Nextflow would re-run in case the samplesheet changes. Nextflow does this natively though

Make nf-core/pixelator compliant with strict syntax

Co-authored-by: Johan Dahlberg <johan@uppsala-bioinformatics.se>

Use $TMPDIR to set temporaryr directories

Enable retry for experiment summary

…0.8.6 Update pixelatorES to 0.8.6

Co-authored-by: Johan Dahlberg <johan@uppsala-bioinformatics.se>

Update documentation to match Proxiome v2 changes

Bump version to 4.0.0

github-actions · 2026-05-19T11:35:29Z

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

Posted for pipeline commit 2e422bc

+| ✅ 229 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   2 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
_
included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ 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: conf/test.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_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: 4.0.0
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= 0.01
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= 10
nextflow_config - Config default value correct: params.pna_graph_component_size_min_threshold= 8000
nextflow_config - Config default value correct: params.pna_sample_calling_remove_incompatible= true
nextflow_config - Config default value correct: params.pna_sample_calling_confidence_threshold= 0.9
nextflow_config - Config default value correct: params.pna_denoise_run_one_core_graph_denoising= true
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_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= wpmds_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.technology= proxiome-v1
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/pixelator/
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/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/nextflow.config' contains modules_testdata_base_path
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 - 'tests/nextflow.config' contains pipelines_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: clean-up.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 = 4.0.0, nfcore_yml.version = 4.0.0

Run details

nf-core/tools version 4.0.2
Run at 2026-05-19 13:10:48

The default volume was decreased from 30 to 40GB

This reverts commit 34a0485.

Fix Singularity CI tests

vagkaratzas

Good stuff. I would suggest sticking to the latest template and using other updated nf-core pipelines as a guide -as much as you can-, so that there is uniformity between pipelines, and no surprises for reviewers, new contributors and users. Take your time and have a look at the comments I left throughout.

Aratz and others added 30 commits March 4, 2026 10:21

Bump version to 3.1.0dev

f51a5f6

Merge pull request #190 from Aratz/post_release3.0.0

5e74a96

Bump version to 3.1.0dev

Merge branch 'master' into back2dev

e3cf2a7

Merge pull request #193 from Aratz/back2dev

955075a

Merge changes from patch 3.0.1 back into dev

Move container env vars to own config

21b8d5e

Remove samplesheet_sha

ef4f36b

As far as I understand, this was set so that Nextflow would re-run in case the samplesheet changes. Nextflow does this natively though

Fix implicit closures

5291f1b

Fix unused parameters

26193f3

Update changelog

061edaa

Standardize option group titles

3b75dc0

Merge pull request #194 from Aratz/pna-2024/fix/strict_syntax

4a80801

Make nf-core/pixelator compliant with strict syntax

Use $TMPDIR to set temporaryr directories

0c1c061

Add container_env.config to nf-test triggers

ef23b1d

Update changelog

044bd48

Add note describing how TMPDIR can be used

f1c38bc

Update docs/usage.md

0fc8d85

Co-authored-by: Johan Dahlberg <johan@uppsala-bioinformatics.se>

Merge pull request #195 from Aratz/feature/pna-2349/use_TMPDIR

7baa67f

Use $TMPDIR to set temporaryr directories

Enable retry for experiment summary

bcdb527

Update changelog

e3e584d

Merge pull request #196 from Aratz/fix/pna-2389/retry_ES

f98b9a5

Enable retry for experiment summary

Update pixelatorES to 0.8.6

8615299

Update changelog

46f9a25

Fix typo

e445087

Merge pull request #197 from Aratz/chore/pna-2385/update_pixelatores_…

e8717b1

…0.8.6 Update pixelatorES to 0.8.6

Template update for nf-core/tools version 4.0.0

48195cd

Template update for nf-core/tools version 4.0.2

2d1043e

Merge branch 'dev' into nf-core-template-merge-4.0.2

3633dfe

Update modules and subworkflows

1b689e5

Fix linting errors

e500e22

Update snapshots

266fe9e

Aratz and others added 17 commits May 19, 2026 10:00

Update changelog

d0ef908

Clarify sample calling output

be7a03a

Co-authored-by: Johan Dahlberg <johan@uppsala-bioinformatics.se>

Improve language

34eeef0

Co-authored-by: Johan Dahlberg <johan@uppsala-bioinformatics.se>

Reorder samplesheet columns in usage.md

33884ac

Co-authored-by: Johan Dahlberg <johan@uppsala-bioinformatics.se>

Specify typical number of hashed samples per pool

b1e2e1b

Co-authored-by: Johan Dahlberg <johan@uppsala-bioinformatics.se>

Clarify row repetition

6157fd5

Co-authored-by: Johan Dahlberg <johan@uppsala-bioinformatics.se>

Clarify parameter description

e0772c3

Co-authored-by: Johan Dahlberg <johan@uppsala-bioinformatics.se>

Remove extra line in README

96b62ed

Co-authored-by: Johan Dahlberg <johan@uppsala-bioinformatics.se>

Improve samplesheet validation

8516df8

Add example with resequenced pools

4759896

Add more samples to example in README

eb04c2b

Add missing warning about new naming scheme

dc26b27

Regenerate ro-crate after readme update

3fecc57

Merge pull request #205 from Aratz/docs/pna-2760/add_docs_v2

29ec0c2

Update documentation to match Proxiome v2 changes

Bump version to 4.0.0

ebe0f58

Update snapshots

df63726

Merge pull request #206 from Aratz/pre-release_4.0.0

e9bdb94

Bump version to 4.0.0

Aratz self-assigned this May 19, 2026

Aratz requested a review from a team as a code owner May 19, 2026 11:33

Aratz mentioned this pull request May 19, 2026

Fix Singularity CI tests #208

Merged

5 tasks

Aratz added 6 commits May 19, 2026 14:42

Increase ci-runner volume back to 40GB

6440495

The default volume was decreased from 30 to 40GB

Temporarily allow singularity tests to run on dev

34a0485

Update changelog

45d53dd

Fix missing changelog entry

825b101

Revert "Temporarily allow singularity tests to run on dev"

ff820cd

This reverts commit 34a0485.

Merge pull request #208 from Aratz/fix/ci_volume

2e422bc

Fix Singularity CI tests

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Release 4.0.0#207

Release 4.0.0#207
Aratz wants to merge 78 commits into
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Aratz commented May 19, 2026 •

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Aratz commented May 19, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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[4.0.0] - 2026-05-19

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Software dependencies

Parameters

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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Aratz commented May 19, 2026 •

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