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Important! Template update for nf-core/tools v4.0.3 - #608

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Important! Template update for nf-core/tools v4.0.3#608
nf-core-bot wants to merge 2 commits into
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nf-core-template-merge-4.0.3

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@nf-core-bot

@nf-core-bot nf-core-bot commented Jul 24, 2026

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Version 4.0.3 of nf-core/tools has just been released with updates to the nf-core template. For more details, check out the blog post: https://nf-co.re/advisories/pr-comment-workflow-vulnerability

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-4.0.3 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 v4.0.3 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.

@github-actions

github-actions Bot commented Jul 31, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

@github-actions

github-actions Bot commented Jul 31, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4691750

+| ✅ 239 tests passed       |+
#| ❔   6 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 base.config: Check the defaults for all processes

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-viralrecon_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-viralrecon_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-viralrecon_logo_dark.png
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/viralrecon/viralrecon/assets/hiv_template_report.html

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-07-31 10:06:18

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@nf-core-bot @LilyAnderssonLee