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Important! Template update for nf-core/tools v3.5.1#937

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dialvarezs merged 5 commits intodevfrom
nf-core-template-merge-3.5.1
Nov 20, 2025
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Important! Template update for nf-core/tools v3.5.1#937
dialvarezs merged 5 commits intodevfrom
nf-core-template-merge-3.5.1

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@nf-core-bot nf-core-bot commented Nov 20, 2025

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: https://nf-co.re/blog/2025/tools-3_5_0

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.

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github-actions Bot commented Nov 20, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1a96418

+| ✅ 382 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • 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
  • 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

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2025-11-20 11:13:01

@dialvarezs
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dialvarezs commented Nov 20, 2025

Thank you @mashehu!

@dialvarezs dialvarezs merged commit baede00 into dev Nov 20, 2025
22 checks passed
@dialvarezs dialvarezs deleted the nf-core-template-merge-3.5.1 branch November 21, 2025 11:35
@dialvarezs dialvarezs mentioned this pull request Dec 1, 2025
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@mashehu mashehu mashehu approved these changes

@jfy133 jfy133 Awaiting requested review from jfy133 jfy133 is a code owner

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

@prototaxites prototaxites Awaiting requested review from prototaxites prototaxites is a code owner

@muabnezor muabnezor Awaiting requested review from muabnezor muabnezor is a code owner

@dialvarezs dialvarezs Awaiting requested review from dialvarezs dialvarezs is a code owner

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@nf-core-bot @dialvarezs @mashehu