Fixed the 4.1.0 template merge

[muffato]

Closes #262

Not the whole 4.1.0 template was applied. This PR addresses that by merging the TEMPLATE branch into dev, resolving conflicts.

I also revamped the test files so that they look exactly the same. – easier to maintain this way

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d6784a4

+| ✅ 229 tests passed       |+
#| ❔  32 tests were ignored |#
!| ❗   8 tests had warnings |!

Details

❗ Test warnings:

• files_exist - File not found: conf/igenomes_ignored.config
• nextflow_config - Config manifest.version should end in dev: 2.1.0
• local_component_structure - change_name.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - merge_output.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - convert_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - align_long.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - align_short.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/multiqc_config.yml
• files_exist - File is ignored: assets/nf-core-readmapping_logo_light.png
• files_exist - File is ignored: assets/methods_description_template.yml
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: docs/images/nf-core-readmapping_logo_dark.png
• files_exist - File is ignored: docs/images/nf-core-readmapping_logo_light.png
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: tower.yml
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• nextflow_config - Config default ignored: params.pacbio_adapter
• nextflow_config - Config default ignored: params.pacbio_adapter_yaml
• files_unchanged - File ignored due to lint config: .gitattributes
• files_unchanged - File does not exist: CODE_OF_CONDUCT.md
• 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/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/config.yml
• 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/email_template.html
• files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
• files_unchanged - File does not exist: assets/nf-core-readmapping_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-readmapping_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-readmapping_logo_dark.png
• files_unchanged - File ignored due to lint config: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/readmapping/readmapping/.github/workflows/awstest.yml
• 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: 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/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: 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/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: conf/base.config
• 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-readmapping_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/WorkflowReadmapping.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.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• 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 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.alignment_format= cram
• nextflow_config - Config default value correct: params.compression= crumble
• nextflow_config - Config default value correct: params.window_size= 1000
• nextflow_config - Config default value correct: params.short_aligner= bwamem2
• nextflow_config - Config default value correct: params.long_reads_map_chunk_size= 10000
• nextflow_config - Config default value correct: params.short_reads_map_chunk_size= 10000
• 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/
• nf_test_content - 'tests/pimms.nf.test' contains outdir parameter
• nf_test_content - 'tests/pimms.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/pimms.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/short_aligner_minimap2.nf.test' contains outdir parameter
• nf_test_content - 'tests/short_aligner_minimap2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/short_aligner_minimap2.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/untrim.nf.test' contains outdir parameter
• nf_test_content - 'tests/untrim.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/untrim.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/amplifi.nf.test' contains outdir parameter
• nf_test_content - 'tests/amplifi.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/amplifi.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/uli.nf.test' contains outdir parameter
• nf_test_content - 'tests/uli.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/uli.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/uli_no_lima.nf.test' contains outdir parameter
• nf_test_content - 'tests/uli_no_lima.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/uli_no_lima.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/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 - .prettierrc.yml matches the template
• files_unchanged - .github/.dockstore.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.txt 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
• 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: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: branch.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: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: sanger_test_full.yml
• actions_schema_validation - Workflow validation passed: sanger_test.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• modules_json - Only installed modules found in modules.json
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• base_config - BLAST_BLASTN found in conf/base.config and Nextflow scripts.
• base_config - BLOBTK_DEPTH found in conf/base.config and Nextflow scripts.
• base_config - BLOBTK_DEPTH found in conf/base.config and Nextflow scripts.
• base_config - BWAMEM2_INDEX found in conf/base.config and Nextflow scripts.
• base_config - CONVERT_CRAM found in conf/base.config and Nextflow scripts.
• base_config - CRUMBLE found in conf/base.config and Nextflow scripts.
• base_config - FASTQC found in conf/base.config and Nextflow scripts.
• base_config - LIMA found in conf/base.config and Nextflow scripts.
• base_config - MINIMAP2_INDEX found in conf/base.config and Nextflow scripts.
• base_config - MULTIQC found in conf/base.config and Nextflow scripts.
• base_config - PBMARKDUP found in conf/base.config and Nextflow scripts.
• base_config - SAMTOOLS_ADDREPLACERG found in conf/base.config and Nextflow scripts.
• base_config - SAMTOOLS_CRAM found in conf/base.config and Nextflow scripts.
• base_config - SAMTOOLS_STATS found in conf/base.config and Nextflow scripts.
• base_config - SAMTOOLS_ found in conf/base.config and Nextflow scripts.
• base_config - SAMTOOLS_ found in conf/base.config and Nextflow scripts.
• base_config - SAMTOOLS_ found in conf/base.config and Nextflow scripts.
• base_config - SAMTOOLS_FASTQ found in conf/base.config and Nextflow scripts.
• base_config - SAMTOOLS_INDEX found in conf/base.config and Nextflow scripts.
• base_config - FASTXALIGN_MINIMAP2ALIGN found in conf/base.config and Nextflow scripts.
• base_config - FASTXALIGN_PYFASTXINDEX found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - BLAST_BLASTN found in conf/modules.config and Nextflow scripts.
• modules_config - BLOBTK_DEPTH found in conf/modules.config and Nextflow scripts.
• modules_config - BGZIP_BEDGRAPH found in conf/modules.config and Nextflow scripts.
• modules_config - CHANGE_NAME found in conf/modules.config and Nextflow scripts.
• modules_config - CONVERT_CRAM found in conf/modules.config and Nextflow scripts.
• modules_config - CRUMBLE found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - GAWK_MODIFY_YAML_BARCODE found in conf/modules.config and Nextflow scripts.
• modules_config - HIFITRIMMER_PROCESSBLAST found in conf/modules.config and Nextflow scripts.
• modules_config - HIFITRIMMER_TRIM found in conf/modules.config and Nextflow scripts.
• modules_config - LIMA found in conf/modules.config and Nextflow scripts.
• modules_config - BLAST_MAKEBLASTDB found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - PBMARKDUP found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_ADDREPLACERG found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FASTQ 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 - SAMTOOLS_MERGEDUP found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_MERGE found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_REHEADER found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_STATS 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: 4.1.0
• 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 4.1.0
• Run at 2026-09-23 09:25:51

[prototaxites]

LGTM. Changelog note about Slack/Teams support?

[muffato]

LGTM. Changelog note about Slack/Teams support?

It's already there ! https://github.com/sanger-tol/readmapping/blob/dev/CHANGELOG.md?plain=1#L13

[prototaxites]

Ah, it doesn't show in the files changed list.

[muffato]

It's because the template 4.1.0 was already applied (#255, #256), though partially. This PR is only for the remaining files that were somehow not patched in the previous PRs. That's also why this PR has got fewer changed files than your typical 4.1.0 template upgrade.