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Important! Template update for nf-core/tools v3.5.1 #42

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Merged
muffato merged 2 commits into from
Dec 2, 2025
Merged

Important! Template update for nf-core/tools v3.5.1 #42

muffato merged 2 commits into from
Dec 2, 2025

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@sanger-tolsoft
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@sanger-tolsoft sanger-tolsoft commented Dec 2, 2025 •
edited by muffato
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Closes #2
Version 3.5.1 of nf-core/tools has just been released with updates to the nf-core template. For more details, check out the blog post: None

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.5.1 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.5.1 release page.

Note

Since nf-core/tools 3.5.0, older template update PRs will not be automatically closed, but will remain open in your pipeline repository. Older template PRs will be automatically closed once a newer template PR has been merged.

@muffato muffato linked an issue Dec 2, 2025 that may be closed by this pull request
Update pipeline template #2
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github-actions bot commented Dec 2, 2025

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 99ff940

+| ✅ 165 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • 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 nextflow.config: Specify any additional parameters here
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/sequencecomposition/sequencecomposition/subworkflows/local/fasta_windows.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
    _
  • local_component_structure - extract_column.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - params_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - fasta_windows.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: assets/nf-core-sequencecomposition_logo_light.png
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • files_exist - File is ignored: docs/images/nf-core-sequencecomposition_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-sequencecomposition_logo_dark.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
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config default ignored: params.selected_fw_output
  • 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/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .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/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-sequencecomposition_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-sequencecomposition_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-sequencecomposition_logo_dark.png
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sequencecomposition/sequencecomposition/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-12-02 10:50:54

@muffato muffato merged commit 614d450 into dev Dec 2, 2025
7 checks passed
@muffato muffato deleted the nf-core-template-merge-3.5.1 branch December 2, 2025 11:00
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Update pipeline template

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@sanger-tolsoft @prototaxites @muffato