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

Nf test #285

Merged
merged 5 commits into from
Apr 23, 2024
Merged

Nf test #285

merged 5 commits into from
Apr 23, 2024

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 added an nf-test for metatdenovo . We should discuss whether we want to use the nf-core/fetchngs method or nf-core/rnaseq. both should be equally valid but they address the test differently. the latter uses snapshots while the other doesn't. which one is our method then? I personally prefer nf-core/fetchngs because it can avoid issues with tools like megahit for md5 files.

@github-actions GitHub Actions
Copy link

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @danilodileo,

It looks like this pull-request is has been made against the danilodileo/metatdenovo master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the danilodileo/metatdenovo dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@danilodileo danilodileo changed the base branch from master to dev April 22, 2024 09:51
@github-actions GitHub Actions
Copy link

github-actions bot commented Apr 22, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4098c2c

+| ✅ 180 tests passed       |+
!| ❗   3 tests had warnings |!

❗ Test warnings:

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

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-23 08:20:01

erikrikarddaniel
erikrikarddaniel approved these changes Apr 23, 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.

👍

@danilodileo danilodileo merged commit 0130295 into nf-core:dev Apr 23, 2024
8 checks passed
@danilodileo danilodileo mentioned this pull request Apr 24, 2024
Merged
11 tasks
@danilodileo danilodileo deleted the nf-test branch April 25, 2024 11:40
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