[mashehu]

This replaces the old fix-linting workflow (.github/workflows/fix_linting.yml, or .github/workflows/fix-linting.yml in pipelines created before nf-core/tools 3.3.0) with .github/workflows/fix-linting.yml, a short stub that calls the reusable fix-linting workflow from nf-core/actions (nf-core/tools#4485).

The old workflow ran the pull request's own lint hooks in a job that also held the nf-core-bot token. The reusable workflow checks who asked for the fix, runs the pull request's code without any secrets, and pushes the result from a separate job that never runs pull request code.

Commenting @nf-core-bot fix linting on a PR works as before. The next template sync makes the same change on dev.

[github-actions]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.2.
Please update your pipeline to the latest version.

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

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 757c0b4

+| ✅ 265 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   6 tests had warnings |!

Details

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 2.0.0
• readme - README did not have a Nextflow minimum version badge.
• readme - README did not have an nf-core template version badge.
• readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
• pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
• pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.

❔ Tests ignored:

• files_exist - File is ignored: .github/workflows/linting_comment.yml
• files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
• files_unchanged - File does not exist: .github/workflows/linting_comment.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ 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/CONTRIBUTING.md
• 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.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-bactmap_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/images/nf-core-bactmap_logo_light.png
• files_exist - File found: docs/images/nf-core-bactmap_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: tests/default.nf.test
• files_exist - File found: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: conf/igenomes.config
• files_exist - File found: conf/igenomes_ignored.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-bactmap_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/WorkflowBactmap.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 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.igenomes_base= s3://ngi-igenomes/igenomes/
• 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.max_multiqc_email_size= 25.MB
• 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/
• nextflow_config - Config default value correct: params.preprocessing_qc_tool= fastqc
• nextflow_config - Config default value correct: params.perform_shortread_qc= true
• nextflow_config - Config default value correct: params.shortread_qc_tool= fastp
• nextflow_config - Config default value correct: params.shortread_qc_minlength= 50
• nextflow_config - Config default value correct: params.perform_longread_qc= true
• nextflow_config - Config default value correct: params.longread_adapterremoval_tool= porechop
• nextflow_config - Config default value correct: params.longread_filter_tool= nanoq
• nextflow_config - Config default value correct: params.longread_qc_qualityfilter_minlength= 1000
• nextflow_config - Config default value correct: params.longread_qc_qualityfilter_keeppercent= 90
• nextflow_config - Config default value correct: params.longread_qc_qualityfilter_targetbases= 500000000
• nextflow_config - Config default value correct: params.longread_qc_qualityfilter_minquality= 7
• nextflow_config - Config default value correct: params.perform_runmerging= true
• nextflow_config - Config default value correct: params.save_runmerged_reads= true
• nextflow_config - Config default value correct: params.perform_subsampling= true
• nextflow_config - Config default value correct: params.subsampling_depth_cutoff= 100
• nextflow_config - Config default value correct: params.shortread_mapping_tool= bowtie2
• nextflow_config - Config default value correct: params.bam_format= true
• nextflow_config - Config default value correct: params.bam_index_extension= bai
• nextflow_config - Config default value correct: params.cigar_bam= true
• nextflow_config - Config default value correct: params.clair3_platform= ont
• nextflow_config - Config default value correct: params.genomecov_threshold= 9
• nextflow_config - Config default value correct: params.genomecov_scale= 1
• nextflow_config - Config default value correct: params.non_GATC_threshold= 0.5
• nf_test_content - 'tests/default.nf.test' contains outdir parameter
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.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 - '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 - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/CONTRIBUTING.md 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/PULL_REQUEST_TEMPLATE.md 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 - assets/nf-core-bactmap_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-bactmap_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-bactmap_logo_dark.png matches the template
• files_unchanged - docs/README.md matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore 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
• 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: pr-comment.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: awstest.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: fix-linting.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - assets/multiqc_config.yml found and not ignored.
• multiqc_config - assets/multiqc_config.yml contains report_section_order
• multiqc_config - assets/multiqc_config.yml contains export_plots
• multiqc_config - assets/multiqc_config.yml contains report_comment
• multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
• multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
• multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
• 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 - BWAMEM2_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQSCAN_RAW found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQSCANPARSE_RAW found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC_PROCESSED found in conf/modules.config and Nextflow scripts.
• modules_config - FALCO found in conf/modules.config and Nextflow scripts.
• modules_config - FALCO_PROCESSED found in conf/modules.config and Nextflow scripts.
• modules_config - FASTP_SINGLE found in conf/modules.config and Nextflow scripts.
• modules_config - FASTP_PAIRED found in conf/modules.config and Nextflow scripts.
• modules_config - ADAPTERREMOVAL_SINGLE found in conf/modules.config and Nextflow scripts.
• modules_config - ADAPTERREMOVAL_PAIRED found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
• modules_config - PORECHOP_PORECHOP found in conf/modules.config and Nextflow scripts.
• modules_config - PORECHOP_ABI found in conf/modules.config and Nextflow scripts.
• modules_config - FILTLONG found in conf/modules.config and Nextflow scripts.
• modules_config - NANOQ found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQSCAN_PROCESSED found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQSCANPARSE_PROCESSED found in conf/modules.config and Nextflow scripts.
• modules_config - READ_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - READSTATS_PARSE found in conf/modules.config and Nextflow scripts.
• modules_config - MERGE_RUNS found in conf/modules.config and Nextflow scripts.
• modules_config - RASUSA found in conf/modules.config and Nextflow scripts.
• modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - BWAMEM2_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FLAGSTAT found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_IDXSTATS found in conf/modules.config and Nextflow scripts.
• modules_config - FREEBAYES found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - MINIMAP2_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - CLAIR3 found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_SORT found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_FILTER found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_NORM found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_QUERY found in conf/modules.config and Nextflow scripts.
• modules_config - BEDTOOLS_GENOMECOV found in conf/modules.config and Nextflow scripts.
• modules_config - BEDTOOLS_SUBTRACT found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_CONSENSUS found in conf/modules.config and Nextflow scripts.
• modules_config - RENAME_FASTA_HEADER found in conf/modules.config and Nextflow scripts.
• modules_config - CONCATENATE_FASTA found in conf/modules.config and Nextflow scripts.
• modules_config - SEQTK_COMP found in conf/modules.config and Nextflow scripts.
• modules_config - SEQTK_PARSE found in conf/modules.config and Nextflow scripts.
• modules_config - ALIGNPSEUDOGENOMES found in conf/modules.config and Nextflow scripts.
• modules_config - SNPSITES found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC 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: 3.5.2
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

• nf-core/tools version 3.5.2
• Run at 2026-10-07 12:51:38