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Important! Template update for nf-core/tools v4.1.0 - #57

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sainsachiko merged 5 commits into
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nf-core-template-merge-4.1.0
Aug 20, 2026
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Important! Template update for nf-core/tools v4.1.0#57
sainsachiko merged 5 commits into
devfrom
nf-core-template-merge-4.1.0

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@sanger-tolsoft

@sanger-tolsoft sanger-tolsoft commented Aug 4, 2026

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Version 4.1.0 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-4.1.0 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 the template sync documentation.

For more information about this release of nf-core/tools, please see the v4.1.0 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 marked this pull request as draft August 18, 2026 08:59
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github-actions Bot commented Aug 19, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c5fdce8

+| ✅ 170 tests passed       |+
#| ❔  24 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   6 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
  • 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: .gitattributes
  • 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/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 fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-08-20 18:33:29

@muffato
muffato marked this pull request as ready for review August 19, 2026 19:49
@sainsachiko
sainsachiko requested a review from muffato August 20, 2026 15:14
muffato
muffato approved these changes Aug 20, 2026
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Comment thread docs/CONTRIBUTING.md Outdated
@sainsachiko @muffato
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c5fdce8 
Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>
@sainsachiko
sainsachiko merged commit 464b9e1 into dev Aug 20, 2026
22 of 28 checks passed
@sainsachiko
sainsachiko deleted the nf-core-template-merge-4.1.0 branch August 20, 2026 20:02
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@sanger-tolsoft @muffato @sainsachiko