Skip to content
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

Update nf-core modules, DADA2, and Phyloseq #720

Merged
merged 7 commits into from
Mar 26, 2024
Merged

Update nf-core modules, DADA2, and Phyloseq #720

merged 7 commits into from
Mar 26, 2024

Conversation

d4straub
Copy link
Collaborator

@d4straub d4straub commented Mar 26, 2024 •
edited
Loading

Software and nf-core module update is due again.

It appears some output changed, multiqc summary in most cases but also cutadapt (v4.0 had the alignemnt changed, that might cause some edge case changes).

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!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/ampliseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@d4straub d4straub added this to the 2.9.0 milestone Mar 26, 2024
@github-actions GitHub Actions
Copy link

github-actions bot commented Mar 26, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 717aa49

+| ✅ 191 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-26 15:38:22

erikrikarddaniel
erikrikarddaniel approved these changes Mar 26, 2024
View reviewed changes
Copy link
Member

@erikrikarddaniel erikrikarddaniel left a comment

Choose a reason for hiding this comment

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

👍

@d4straub
Copy link
Collaborator Author

Thanks!

@d4straub d4straub merged commit 43378b5 into nf-core:dev Mar 26, 2024
17 checks passed
@d4straub d4straub deleted the update-modules branch March 26, 2024 16:00
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
2.9.0
Development

Successfully merging this pull request may close these issues.
2 participants
@d4straub @erikrikarddaniel