Release 5.0.1 by Aratz · Pull Request #244 · nf-core/pixelator

Aratz · 2026-08-19T14:37:42Z

[5.0.1] - 2026-08-17

Patches

Changed

Increase pna_graph_component_size_max_threshold default value to 1M. By @Aratz #243

Documentation

Document how to configure DuckDB temporary storage environment variables. By @johandahlberg #238

Bug fixes

Configure container override for sample calling step. By @Aratz #241

Infrastructure

Update nf-core template to 4.0.3 by @Aratz #236
Automate release creation. By @Aratz #235
Automate post-release backsync to dev. By @Aratz #239
Bump setup-apptainer back to latest version. By @Aratz #245

Software dependencies

Dependency	Old version	New version
`pixelator`	0.29.0	0.30.0
`pixelatorES`	0.11.2	0.12.0

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Post-release 5.0.0

Automate release creation

…-4.0.3

Important! Template update for nf-core/tools v4.0.3

Co-authored-by: Cursor <cursoragent@cursor.com>

Co-authored-by: Adrien Coulier <adrien.coulier@pixelgen.com>

Automate back sync to dev after release

Document DuckDB temporary storage environment variables.

These files now contain input/output path, with will typically change between runs.

Update pixelator

Fix container override in sample calling

Increase pna_graph_component_size_max_threshold default to 1M

Pre release 5.0.1

github-actions · 2026-08-19T14:38:31Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

github-actions · 2026-08-19T14:43:32Z

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

Posted for pipeline commit 81ed0ca

+| ✅ 233 tests passed       |+
#| ❔  12 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_exist - File is ignored: .github/workflows/linting_comment.yml
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: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
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/pr-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: 5.0.1
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= 1000000
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/pr-comment.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: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: release.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: pr-comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: post-release-sync.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: 4.0.3
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 5.0.1, nfcore_yml.version = 5.0.1
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 4.0.3
Run at 2026-08-20 13:32:13

github-actions · 2026-08-19T14:46:50Z

❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

❌ singularity | latest-everything | Shard 4/7

See the full run for details.

This reverts commit f257d7f.

Update README.md

Fix singularity ci tests

Aratz and others added 30 commits July 16, 2026 13:27

Bump version to 5.1.0dev

755ef9e

Update CHANGELOG.md

00df14a

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Merge pull request #234 from Aratz/bump_5.1.0dev

e408fc3

Post-release 5.0.0

Add release workflow

1d0f4e8

Update changelog

4753cd8

Document automation in contributing guidelines

ca3965a

Merge pull request #235 from Aratz/feature/auto_release

53d856c

Automate release creation

Template update for nf-core/tools version 4.0.3

e72e13e

Merge remote-tracking branch 'origin/dev' into nf-core-template-merge…

277d4f0

…-4.0.3

Merge pull request #236 from nf-core/nf-core-template-merge-4.0.3

2935206

Important! Template update for nf-core/tools v4.0.3

Document DuckDB temporary storage environment variables.

6f5f693

Co-authored-by: Cursor <cursoragent@cursor.com>

Update changelog with pr nbr

217ac61

Update docs/usage.md

deaaa26

Co-authored-by: Adrien Coulier <adrien.coulier@pixelgen.com>

Automate back sync to dev after release

c3912d3

Update documentation

ecec143

Update changelog

3210936

Merge pull request #239 from Aratz/feature/auto_backsync

ee62b07

Automate back sync to dev after release

Merge branch 'dev' into add-info-on-tmp-dir-env-vars

1619984

Fix formatting

1d7ba64

Merge pull request #238 from nf-core/add-info-on-tmp-dir-env-vars

fb54d3d

Document DuckDB temporary storage environment variables.

Update pixelator to 0.30.0

4fc8f13

Update pixelatorES to 0.12.0

322caf3

Migrate pixelator/sample_calling to version topic

a055c60

Update changelog

1e4ca47

Update snapshots

c42a315

Remove meta files from snapshot

a429349

These files now contain input/output path, with will typically change between runs.

Merge pull request #240 from Aratz/update_pixelator

81e0d34

Update pixelator

Fix container override in sample calling

10a6903

Update changelog

8f1f9b3

Merge pull request #241 from Aratz/fix/sample_calling_container

b6bcc6d

Fix container override in sample calling

Aratz added 6 commits August 17, 2026 13:33

Increase pna_graph_component_size_max_threshold to 1M

5554b47

Update changelog

e2a8012

Merge pull request #243 from Aratz/fix/pna-3316_max_cells_threshold

6419699

Increase pna_graph_component_size_max_threshold default to 1M

Finalize changelog

57d7023

Bump version to 5.0.1

a8df0e8

Merge pull request #242 from Aratz/pre-release_5.0.1

46c0e22

Pre release 5.0.1

Aratz self-assigned this Aug 19, 2026

Aratz requested a review from a team as a code owner August 19, 2026 14:37

johandahlberg approved these changes Aug 19, 2026

View reviewed changes

ptajvar approved these changes Aug 19, 2026

View reviewed changes

Aratz added 2 commits August 20, 2026 08:12

Temporarily allow singularity tests to run on dev

f257d7f

Bump setup-apptainer to latest

216b484

Aratz mentioned this pull request Aug 20, 2026

Fix singularity ci tests #245

Merged

4 tasks

Aratz and others added 5 commits August 20, 2026 08:36

Revert "Temporarily allow singularity tests to run on dev"

04244ab

This reverts commit f257d7f.

Update changelog

ee3337d

Update README.md

071ad40

Merge pull request #246 from nf-core/fix-wrong-parameter-value-in-readme

63e5acd

Update README.md

Merge pull request #245 from Aratz/dev

81ed0ca

Fix singularity ci tests

Aratz merged commit eb3757a into master Aug 20, 2026
35 of 36 checks passed

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Release 5.0.1 - #244

Release 5.0.1#244
Aratz merged 43 commits into
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Aratz commented Aug 19, 2026 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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[5.0.1] - 2026-08-17

Patches

Changed

Documentation

Bug fixes

Infrastructure

Software dependencies

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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❌ nf-test failed with latest Nextflow version

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Aratz commented Aug 19, 2026 •

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

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