[Aratz]

[6.0.0] - 2026-11-02

Major

Enhancements & fixes

• Update pixelator to 0.31.0. By @Aratz #270

Patches

Enhancements & fixes

• Setup AWS megatests. By @Aratz #267
• Update nf-core template to 4.2.1 by @Aratz #269
• Update pixelatorES to 0.15.1. By @Aratz #270

Parameters

Old parameter	New parameter
--pna_analysis_proximity_nbr_of_permutations

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	0.30.0	0.31.0
pixelatorES	0.11.2	0.15.1

[github-actions]

nf-core pipelines lint overall result: Passed ✅

Posted for pipeline commit f6e379b

+| ✅ 235 tests passed       |+
#| ❔  12 tests were ignored |#

Details

❔ 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: manifest.diagram
• 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 manifest.homePage began with https://github.com/nf-core/
• nextflow_config - Config dag.file ended with .html
• nextflow_config - Config manifest.diagram file found: docs/images/nf-core-pixelator-metromap.svg
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version does not contain dev for release: 6.0.0
• 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= 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_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
• pipeline_if_empty_null - No ifEmpty(null) 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: awstest.yml
• actions_schema_validation - Workflow validation passed: pr-comment.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: release.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: post-release-sync.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: 4.2.1
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
• version_consistency - Version tags are consistent: manifest.version = 6.0.0, nfcore_yml.version = 6.0.0
• included_configs - Pipeline config includes custom configs.

Run details

• nf-core/tools version 4.2.1
• Run at 2026-11-02 10:38:32