Skip to content

Release 1.3.1 - #289

Merged
erikrikarddaniel merged 8 commits into
nf-core:masterfrom
erikrikarddaniel:patch
Oct 22, 2026
Merged

Release 1.3.1#289
erikrikarddaniel merged 8 commits into
nf-core:masterfrom
erikrikarddaniel:patch

Conversation

@erikrikarddaniel

@erikrikarddaniel erikrikarddaniel commented Oct 21, 2026

Copy link
Copy Markdown
Member

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nf-test test --tag pipeline --profile=+docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

Description

Patch release 1.3.1, with three fixes cherry-picked from dev onto the 1.3.0 tag:

Everything else on dev (the HMM profile search, the nf-core modules update) stays for the next minor release.
The branch also has the version bump to 1.3.1, the CHANGELOG handles and the pipeline version in the test snapshots.

The full pipeline test suite passes except annotator: bakta_supported_only.
That test fails on the magmap.proteins.faa.gz md5 when run on one machine, which this change does not touch.
The release date in the CHANGELOG will be set just before merging.

🤖 Generated with Claude Code

https://claude.ai/code/session_01UvGYU6kuXJeVv9ffdSzdzH

danilodileo and others added 7 commits October 21, 2026 12:53
@danilodileo @erikrikarddaniel
Merge pull request nf-core#277 from danilodileo/fix-apptainer-contain…
7572135 
…er-selection

Accept Apptainer in the container selection of local modules
@erikrikarddaniel
Merge pull request nf-core#284 from erikrikarddaniel/duckdb-feature-c…
6861c80 
…ounts

Split and join the feature counts in DuckDB
@erikrikarddaniel
Merge pull request nf-core#287 from erikrikarddaniel/typed-params
78adfff 
Declare the types of the boolean and numeric params in main.nf
@erikrikarddaniel @claude
Bump version to 1.3.1
961ea3e 
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01UvGYU6kuXJeVv9ffdSzdzH
@erikrikarddaniel @claude
Name authors and reviewers in the CHANGELOG entries
40154e5 
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01UvGYU6kuXJeVv9ffdSzdzH
@erikrikarddaniel @claude
Update the pipeline version in the test snapshots to 1.3.1
04022a6 
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01UvGYU6kuXJeVv9ffdSzdzH
@erikrikarddaniel @claude
Fix comments and test-profile headers
6af8988 
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01UvGYU6kuXJeVv9ffdSzdzH
@github-actions

github-actions Bot commented Oct 21, 2026

Copy link
Copy Markdown

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.1.0.
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 Oct 21, 2026 •
edited
Loading

Copy link
Copy Markdown

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 092509f

+| ✅ 287 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/nf-core-magmap_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-magmap_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-10-22 09:39:22

@erikrikarddaniel
erikrikarddaniel marked this pull request as ready for review October 21, 2026 16:07
mashehu
mashehu requested changes Oct 22, 2026
View reviewed changes

@mashehu mashehu left a comment

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

this should go the usual release path: random-branch->dev->master. patch-> master should only be used in exceptional cases, e.g. security fixes. Don't see this is the case here

@erikrikarddaniel

erikrikarddaniel commented Oct 22, 2026 •
edited
Loading

Copy link
Copy Markdown
Member Author

this should go the usual release path: random-branch->dev->master. patch-> master should only be used in exceptional cases, e.g. security fixes. Don't see this is the case here

#287 is certainly not a security fix, but an important fix for command line users. There is more work on dev that is waiting for other work which would delay the release of this. #277 and #284 are less important, but isolated from the other work on dev.

Moreover, all three went from topic -> dev -> patch so they've seen the same review as everything else. They were cherry-picked from dev to patch.

mashehu
mashehu approved these changes Oct 22, 2026
View reviewed changes

@mashehu mashehu left a comment

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Okay, since they are all cherry-picked from dev I guess it is almost the same.

If you have users running into this, they should move things into a params.yml and it should be fine (which is anyway a more reproducible way to do things), see https://nf-co.re/blog/2026/parameter-types

Comment thread CHANGELOG.md Outdated
@erikrikarddaniel

erikrikarddaniel commented Oct 22, 2026

Copy link
Copy Markdown
Member Author

Okay, since they are all cherry-picked from dev I guess it is almost the same.

If you have users running into this, they should move things into a params.yml and it should be fine (which is anyway a more reproducible way to do things), see https://nf-co.re/blog/2026/parameter-types

I agree, and of course practice this myself, but it should still work as advertised.

ramprasadn
ramprasadn approved these changes Oct 22, 2026
View reviewed changes

@ramprasadn ramprasadn left a comment

Copy link
Copy Markdown

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM! One thing though, should this be a minor release? It seems to involve more than a bug fix.

@erikrikarddaniel

erikrikarddaniel commented Oct 22, 2026

Copy link
Copy Markdown
Member Author

LGTM! One thing though, should this be a minor release? It seems to involve more than a bug fix.

It is a couple of bug fixes IMO, but I see your point. See also my discussion with Matthias.

@ramprasadn

ramprasadn commented Oct 22, 2026

Copy link
Copy Markdown

Oops. Missed it. Sounds good to me 👍🏻 🚀

erikrikarddaniel
erikrikarddaniel commented Oct 22, 2026
View reviewed changes
Comment thread CHANGELOG.md Outdated
@erikrikarddaniel
erikrikarddaniel merged commit 8396600 into nf-core:master Oct 22, 2026
36 checks passed
@erikrikarddaniel
erikrikarddaniel deleted the patch branch October 22, 2026 09:39
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@mashehu mashehu mashehu approved these changes
@ramprasadn ramprasadn ramprasadn approved these changes

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

4 participants

@erikrikarddaniel @ramprasadn @mashehu @danilodileo