[mashehu]

Security patch

This PR applies a security fix included in nf-core/tools 4.0.3 for a potential exploit in the GitHub Actions workflows that post comments on pull requests.

For details, see the related security advisory: https://nf-co.re/advisories/pr-comment-workflow-vulnerability

The fix must be merged into the default branch to take effect. Please merge this PR as soon as possible.

These changes only affect CI workflows, so merging them into the default branch does not require a new pipeline release.

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.2.
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 a7b9dba

+| ✅ 258 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   4 tests had warnings |!

Details

❗ Test warnings:

• pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
• pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/magmap/magmap/lint_results.md: _* pipeline_if_empty_null - No ifEmpty(null) strings found
  _
• schema_lint - Input mimetype is missing or empty
• included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ 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
• files_unchanged - File ignored due to lint config: assets/nf-core-magmap_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_dark.png

✅ 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.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-magmap_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-magmap_logo_light.png
• files_exist - File found: docs/images/nf-core-magmap_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-magmap_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/WorkflowMagmap.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: 1.1.0
• 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.remote_genome_sources= https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt,https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_genbank.txt
• nextflow_config - Config default value correct: params.genome_store_dir= magmap_genomes
• nextflow_config - Config default value correct: params.prokka_store_dir= magmap_prokka
• nextflow_config - Config default value correct: params.bbmap_minid= 0.9
• nextflow_config - Config default value correct: params.bbmap_ambiguous= best
• nextflow_config - Config default value correct: params.features= CDS,rRNA,tRNA,tmRNA
• nextflow_config - Config default value correct: params.genomeset_mode= joint
• nextflow_config - Config default value correct: params.skip_sourmash= true
• nextflow_config - Config default value correct: params.sourmash_ksize= 21
• 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/
• nf_test_content - 'tests/single.nf.test' contains outdir parameter
• nf_test_content - 'tests/single.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/single.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/duplicates.nf.test' contains outdir parameter
• nf_test_content - 'tests/duplicates.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/duplicates.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sourmash_mix.nf.test' contains outdir parameter
• nf_test_content - 'tests/sourmash_mix.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sourmash_mix.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sourmash.nf.test' contains outdir parameter
• nf_test_content - 'tests/sourmash.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sourmash.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sourmash_10genomes_joint.nf.test' contains outdir parameter
• nf_test_content - 'tests/sourmash_10genomes_joint.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sourmash_10genomes_joint.nf.test' snapshots a 'versions.yml' file
• 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/sourmash_10genomes_sample.nf.test' contains outdir parameter
• nf_test_content - 'tests/sourmash_10genomes_sample.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sourmash_10genomes_sample.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sourmash_mix_sampleset.nf.test' contains outdir parameter
• nf_test_content - 'tests/sourmash_mix_sampleset.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/sourmash_mix_sampleset.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/metadata.nf.test' contains outdir parameter
• nf_test_content - 'tests/metadata.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/metadata.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/skip_preprocessing_steps.nf.test' contains outdir parameter
• nf_test_content - 'tests/skip_preprocessing_steps.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/skip_preprocessing_steps.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/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 - 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
• 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.
• 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_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.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: pr-comment.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: release-announcements.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
• 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 - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - TRIMGALORE found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_MANY found in conf/modules.config and Nextflow scripts.
• modules_config - GENOMES2ORFS found in conf/modules.config and Nextflow scripts.
• modules_config - BAM_SORT_STATS_SAMTOOLS found in conf/modules.config and Nextflow scripts.
• modules_config - WGET_GENOME found in conf/modules.config and Nextflow scripts.
• modules_config - PROKKAGFF2TSV found in conf/modules.config and Nextflow scripts.
• modules_config - PROKKA found in conf/modules.config and Nextflow scripts.
• modules_config - CATPROKKATSVS found in conf/modules.config and Nextflow scripts.
• modules_config - SAMPLE_SKETCH found in conf/modules.config and Nextflow scripts.
• modules_config - GENOME_SKETCH found in conf/modules.config and Nextflow scripts.
• modules_config - GENOME_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - SOURMASH_GATHER found in conf/modules.config and Nextflow scripts.
• modules_config - SOURMASH_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - BBMAP_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - BBMAP_ALIGN 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 - COLLECT_FEATURECOUNTS found in conf/modules.config and Nextflow scripts.
• modules_config - TIDYVERSE_JOINMETADATA found in conf/modules.config and Nextflow scripts.
• modules_config - COLLECT_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_DUMPSOFTWAREVERSIONS 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: 4.0.2
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
• container_configs - conf/containers_conda_lock_files_amd64.config is up to date
• container_configs - conf/containers_conda_lock_files_arm64.config is up to date
• container_configs - conf/containers_docker_amd64.config is up to date
• container_configs - conf/containers_docker_arm64.config is up to date
• container_configs - conf/containers_singularity_https_amd64.config is up to date
• container_configs - conf/containers_singularity_https_arm64.config is up to date
• container_configs - conf/containers_singularity_oras_amd64.config is up to date
• container_configs - conf/containers_singularity_oras_arm64.config is up to date
• version_consistency - Version tags are consistent: manifest.version = 1.1.0, nfcore_yml.version = 1.1.0

Run details

• nf-core/tools version 4.0.2
• Run at 2026-07-24 14:26:04