Skip to content

Important! Template update for nf-core/tools v3.5.1 #129

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
AlexBarbera merged 3 commits into from
Jan 23, 2026
Merged

Important! Template update for nf-core/tools v3.5.1 #129

AlexBarbera merged 3 commits into from
Jan 23, 2026

Conversation

@nf-core-bot
Copy link
Member

@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.

@github-actions
Copy link

github-actions bot commented Dec 17, 2025 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d565f3e

+| ✅ 223 tests passed       |+
#| ❔   5 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.0.0
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_lint - Parameter input not found in schema

❔ 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: .gitignore or .prettierignore
  • template_strings - Ignoring Jinja template strings in file /home/runner/work/mcmicro/mcmicro/assets/mcmicro_metro.pdf

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-01-23 20:45:07

@AlexBarbera AlexBarbera requested a review from jmuhlich December 18, 2025 15:09
@AlexBarbera AlexBarbera self-assigned this Jan 23, 2026
@AlexBarbera AlexBarbera merged commit d27bf2c into dev Jan 23, 2026
20 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@AlexBarbera AlexBarbera AlexBarbera approved these changes

@jmuhlich jmuhlich Awaiting requested review from jmuhlich

Assignees

@AlexBarbera AlexBarbera

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

3 participants

@nf-core-bot @AlexBarbera