Update aligners (bwa, bowtie2, chromap and star)

[Kevin-Brockers]

This is a bit of a bigger PR - see here: #522

PR checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• CHANGELOG.md is updated.

[Kevin-Brockers]

I'm currently fixing a few more things - e.g: when using chromap the pipeline currently fails since chromap does not add readgroups by default and picard markduplicates currently fails.

I'm on it see here: nf-core/modules#12283

Therefore the tests are currently failing

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 44328ed

+| ✅ 271 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   8 tests had warnings |!

Details

❗ Test warnings:

• 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 nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
• pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
• pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
• pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
• pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
• pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
• pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

• nextflow_config - Config default ignored: params.bamtools_filter_pe_config
• nextflow_config - Config default ignored: params.bamtools_filter_se_config
• files_unchanged - File ignored due to lint config: assets/nf-core-chipseq_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-chipseq_logo_dark.png
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• merge_markers - Ignoring file /home/runner/work/chipseq/chipseq/modules/nf-core/bowtie2/align/tests/main.nf.test.snap

✅ 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-chipseq_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-chipseq_logo_light.png
• files_exist - File found: docs/images/nf-core-chipseq_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-chipseq_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/WorkflowChipseq.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 ends in dev: 2.2.0dev
• 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.fragment_size= 200
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
• nextflow_config - Config default value correct: params.aligner= bwa
• nextflow_config - Config default value correct: params.broad_cutoff= 0.1
• nextflow_config - Config default value correct: params.min_reps_consensus= 1
• nextflow_config - Config default value correct: params.skip_preseq= true
• nextflow_config - Config default value correct: params.deseq2_vst= 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.fingerprint_bins= 500000
• 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/star.nf.test' contains outdir parameter
• nf_test_content - 'tests/star.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/star.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/star.nf.test' contains outdir parameter
• nf_test_content - 'tests/skip_trimming.nf.test' contains outdir parameter
• nf_test_content - 'tests/skip_trimming.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/skip_trimming.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/skip_trimming.nf.test' contains outdir parameter
• nf_test_content - 'tests/skip_consensus_peaks.nf.test' contains outdir parameter
• nf_test_content - 'tests/skip_consensus_peaks.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/skip_consensus_peaks.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/skip_consensus_peaks.nf.test' contains outdir parameter
• 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/bowtie2.nf.test' contains outdir parameter
• nf_test_content - 'tests/bowtie2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/bowtie2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/bowtie2.nf.test' contains outdir parameter
• nf_test_content - 'tests/chromap.nf.test' contains outdir parameter
• nf_test_content - 'tests/chromap.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/chromap.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/chromap.nf.test' contains outdir parameter
• 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 - .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-chipseq_logo_light.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_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: nf-test.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.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 - SAMPLESHEET_CHECK found in conf/modules.config and Nextflow scripts.
• modules_config - KHMER_UNIQUEKMERS found in conf/modules.config and Nextflow scripts.
• modules_config - GUNZIP_ found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR_ found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - GFFREAD found in conf/modules.config and Nextflow scripts.
• modules_config - GTF2BED found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
• modules_config - GENOME_BLACKLIST_REGIONS found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - TRIMGALORE found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - CHROMAP_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - CHROMAP_CHROMAP found in conf/modules.config and Nextflow scripts.
• modules_config - PICARD_MERGESAMFILES found in conf/modules.config and Nextflow scripts.
• modules_config - BAMTOOLS_FILTER found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CHIPSEQ found in conf/modules.config and Nextflow scripts.
• modules_config - BAM_REMOVE_ORPHANS found in conf/modules.config and Nextflow scripts.
• modules_config - PHANTOMPEAKQUALTOOLS found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS found in conf/modules.config and Nextflow scripts.
• modules_config - PICARD_COLLECTMULTIPLEMETRICS found in conf/modules.config and Nextflow scripts.
• modules_config - PRESEQ_LCEXTRAP found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPTOOLS_COMPUTEMATRIX found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPTOOLS_PLOTPROFILE found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPTOOLS_PLOTHEATMAP found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPTOOLS_PLOTFINGERPRINT found in conf/modules.config and Nextflow scripts.
• modules_config - MACS3_CALLPEAK found in conf/modules.config and Nextflow scripts.
• modules_config - FRIP_SCORE found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC_CUSTOM_PEAKS found in conf/modules.config and Nextflow scripts.
• modules_config - PLOT_MACS3_QC found in conf/modules.config and Nextflow scripts.
• modules_config - PLOT_HOMER_ANNOTATEPEAKS found in conf/modules.config and Nextflow scripts.
• modules_config - MACS3_CONSENSUS found in conf/modules.config and Nextflow scripts.
• modules_config - SUBREAD_FEATURECOUNTS found in conf/modules.config and Nextflow scripts.
• modules_config - ANNOTATE_BOOLEAN_PEAKS found in conf/modules.config and Nextflow scripts.
• modules_config - DESEQ2_QC found in conf/modules.config and Nextflow scripts.
• modules_config - IGV 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

Run details

• nf-core/tools version 4.0.2
• Run at 2026-07-08 22:25:23