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Important! Template update for nf-core/tools v4.0.3 - #90

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KateSakharova merged 4 commits into
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nf-core-template-merge-4.0.3
Jul 30, 2026
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Important! Template update for nf-core/tools v4.0.3#90
KateSakharova merged 4 commits into
1.0.0from
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.

@KateSakharova
KateSakharova changed the base branch from dev to 1.0.0 July 29, 2026 08:49
@github-actions

github-actions Bot commented Jul 30, 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 30, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit decd115

+| ✅ 251 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/igenomes_ignored.config
  • nextflow_config - Config variable ignored: params.input
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-seqsubmit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-seqsubmit_logo_dark.png
  • container_configs - container_configs

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.0.3
  • Run at 2026-07-30 13:46:52

This was referenced Jul 30, 2026
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@KateSakharova
KateSakharova merged commit 5673e5b into 1.0.0 Jul 30, 2026
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@KateSakharova
KateSakharova deleted the nf-core-template-merge-4.0.3 branch July 30, 2026 13:48
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@nf-core-bot @KateSakharova