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

Modified tree structure #332

Merged
merged 9 commits into from
Feb 11, 2025
Merged

Modified tree structure #332

merged 9 commits into from
Feb 11, 2025

Conversation

danilodileo
Copy link
Collaborator

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/metatdenovo 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).

I removed most of the warnings and also updated the modules.

some warnings remain tough.. I can fix them next PR

@github-actions GitHub Actions
Copy link

github-actions bot commented Feb 7, 2025 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 72826b0

+| ✅ 238 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • system_exit - System.exit in NfcoreSchema.groovy: System.exit(1) [line 180]

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-02-07 15:10:27

erikrikarddaniel
erikrikarddaniel approved these changes Feb 7, 2025
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.

Herculean job! :-)
Did you try any test with Conda? As I see it, that's a possible problem since you've moved that to the environment.yml files.

@danilodileo
Copy link
Collaborator Author

Herculean job! :-) Did you try any test with Conda? As I see it, that's a possible problem since you've moved that to the environment.yml files.

Haven't tried yet as I never used conda profile. I can test it right now.

@danilodileo
Copy link
Collaborator Author

Conda options seem to work fine. I'll merge it.

@danilodileo danilodileo merged commit 18886a5 into nf-core:dev Feb 11, 2025
6 checks passed
@danilodileo danilodileo mentioned this pull request Feb 11, 2025
Closed
@danilodileo danilodileo deleted the modified-tree-structure branch February 11, 2025 09:36
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
No milestone
Development

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