Template update for nf-core/tools v4.1.0 by erikrikarddaniel · Pull Request #68 · nf-core/phyloplace

erikrikarddaniel · 2026-08-03T07:16:51Z

PR checklist

Description

Template update to nf-core/tools v4.1.0 (nf-core pipelines sync), plus nf-core modules update --all --no-preview / nf-core subworkflows update --all --no-preview (no module content changes; only subworkflows/nf-core/utils_nextflow_pipeline's tracked commit pin moved). No tool/software versions changed, so CHANGELOG.md's Dependencies table stays empty.

Notable conflict resolutions during the merge:

Dropped FASTQC-related lines the template scaffold reintroduces in conf/containers_*.config — this pipeline doesn't use the FASTQC module (matches existing convention).
Adopted the template's fix for conf/containers_conda_lock_files_*.config, which now correctly assigns the conda-lock file path to the conda directive instead of container.
The eWaterCycle/setup-apptainer digest in .github/actions/nf-test/action.yml in the new template now matches the pre-4.0.3 digest we'd already manually reverted to (nf-core/tools 4.1.0 fixed this upstream) — removed our now-redundant workaround comment.
Kept our own ## v2.2.0dev CHANGELOG section instead of the template's initial-release boilerplate.

nf-core pipelines lint and nextflow lint . (both min declared 25.10.4 and latest 26.04.6) pass clean; the one nextflow lint error under 25.10.4 (utils_nextflow_pipeline/main.nf, groovy.json.JsonGenerator.Options) is pre-existing vendored code unrelated to this sync and disappears entirely under 26.04.6, confirming it's a linter/version limitation rather than a real bug.

github-actions · 2026-08-03T07:18:38Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit b02ece0

+| ✅ 228 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   1 tests had warnings |!

Details

❗ Test warnings:

schema_lint - Parameter input not found in schema

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: .github/workflows/linting_comment.yml
nextflow_config - Config variable ignored: params.input
files_unchanged - File ignored due to lint config: .gitattributes
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-phyloplace_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-phyloplace_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-phyloplace_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/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-phyloplace_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-phyloplace_logo_light.png
files_exist - File found: docs/images/nf-core-phyloplace_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: .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-phyloplace_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/WorkflowPhyloplace.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: 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 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.id= placement
nextflow_config - Config default value correct: params.alignmethod= hmmer
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/hmmfile.nf.test' contains outdir parameter
nf_test_content - 'tests/hmmfile.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hmmfile.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/clustalo.nf.test' contains outdir parameter
nf_test_content - 'tests/clustalo.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/clustalo.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/phylosearch_input.nf.test' contains outdir parameter
nf_test_content - 'tests/phylosearch_input.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/phylosearch_input.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/phyloplace_input.nf.test' contains outdir parameter
nf_test_content - 'tests/phyloplace_input.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/phyloplace_input.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mafft.nf.test' contains outdir parameter
nf_test_content - 'tests/mafft.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/mafft.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 - 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/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/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.
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_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 - HMMER_HMMSEARCH found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_HMMBUILD found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_UNALIGNREF found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_HMMALIGNREF found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_HMMALIGNQUERY found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_MASK found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_MASKQUERY found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_MASKREF found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_AFAFORMATQUERY found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_AFAFORMATREF found in conf/modules.config and Nextflow scripts.
modules_config - MAFFT found in conf/modules.config and Nextflow scripts.
modules_config - EPANG_PLACE found in conf/modules.config and Nextflow scripts.
modules_config - GAPPA_GRAFT found in conf/modules.config and Nextflow scripts.
modules_config - GAPPA_ASSIGN found in conf/modules.config and Nextflow scripts.
modules_config - GAPPA_HEATTREE 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: 4.1.0
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 2026-08-03 09:55:03

…ers stuck queued)

piplus2

LGTM you don't keep track of template sync in the changelog?

erikrikarddaniel · 2026-08-03T09:51:21Z

LGTM you don't keep track of template sync in the changelog?

I should, thanks for catching that.

erikrikarddaniel added 4 commits August 3, 2026 08:52

Template update for nf-core/tools version 4.1.0

7d33f0e

Merge TEMPLATE into template-update-4.1.0

13329cd

Update subworkflows/nf-core/utils_nextflow_pipeline pin

9844bba

Fix RO-Crate description sync (nf-core pipelines lint --fix)

822a851

Try GitHub-hosted ubuntu-latest runners for nf-test (self-hosted runn…

0a52d88

…ers stuck queued)

erikrikarddaniel marked this pull request as ready for review August 3, 2026 08:27

piplus2 approved these changes Aug 3, 2026

View reviewed changes

Add CHANGELOG entry for the 4.1.0 template update

b02ece0

erikrikarddaniel merged commit 9c5b490 into nf-core:dev Aug 3, 2026
17 checks passed

erikrikarddaniel deleted the template-update-4.1.0 branch August 3, 2026 09:56

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Template update for nf-core/tools v4.1.0 - #68

Template update for nf-core/tools v4.1.0#68
erikrikarddaniel merged 6 commits into
nf-core:devfrom
erikrikarddaniel:template-update-4.1.0

erikrikarddaniel commented Aug 3, 2026

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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erikrikarddaniel commented Aug 3, 2026

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erikrikarddaniel commented Aug 3, 2026

PR checklist

Description

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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erikrikarddaniel commented Aug 3, 2026

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github-actions Bot commented Aug 3, 2026 •

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️