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Important! Template update for nf-core/tools v4.0.3 - #305

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nictru merged 2 commits into
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nf-core-template-merge-4.0.3
Jul 26, 2026
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Important! Template update for nf-core/tools v4.0.3#305
nictru merged 2 commits into
devfrom
nf-core-template-merge-4.0.3

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@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.

@nf-core-bot
nf-core-bot requested a review from nictru as a code owner July 24, 2026 12:37
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github-actions Bot commented Jul 26, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 71449f8

+| ✅ 314 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  15 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-07-26 10:50:53

@nictru
nictru merged commit 560853d into dev Jul 26, 2026
57 checks passed
@nictru
nictru deleted the nf-core-template-merge-4.0.3 branch July 26, 2026 16:40
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@nictru nictru nictru approved these changes

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