8000 Migrate pytest aligner and pipeline default tests to nf-test by maxulysse · Pull Request #1678 · nf-core/sarek · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

Migrate pytest aligner and pipeline default tests to nf-test #1678

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. W 8000 e’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
merged 25 commits into from
Oct 23, 2024
Merged

Migrate pytest aligner and pipeline default tests to nf-test #1678

merged 25 commits into from
Oct 23, 2024

Conversation

maxulysse
Copy link
Member

Replace #1675

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/sarek 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).

@maxulysse maxulysse changed the base branch from master to dev October 8, 2024 05:41
@github-actions GitHub Actions
Copy link
github-actions bot commented Oct 8, 2024 •
edited
Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fb9b6ee

+| ✅ 214 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-23 10:25:17

@maxulysse maxulysse changed the title Migrate pytest aligner tests to nf-test Migrate pytest aligner and pipeline default tests to nf-test Oct 8, 2024
@nf-core nf-core deleted a comment from github-actions bot Oct 8, 2024
nvnieuwk
nvnieuwk previously approved these changes Oct 8, 2024
View reviewed changes
Copy link
@nvnieuwk nvnieuwk left a comment

Choose a reason for hiding this comment

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

This looks so beautiful!

@maxulysse maxulysse mentioned this pull request Oct 8, 2024
Merged
11 tasks
@fellen31 fellen31 mentioned this pull request Oct 8, 2024
Closed
2 tasks
@maxulysse maxulysse mentioned this pull request Oct 11, 2024
Merged
maxulysse
maxulysse commented Oct 23, 2024
View reviewed changes
@nf-core-bot
Copy link
Member

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@maxulysse
Copy link
Member Author

THANK YOU SO MUCH @FriederikeHanssen

@maxulysse maxulysse merged commit 100258d into nf-core:dev Oct 23, 2024
15 checks passed
@maxulysse maxulysse deleted the nft-utils-0-0-3 branch October 23, 2024 10:43
@maxulysse maxulysse mentioned this pull request Apr 30, 2025
Open
27 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@nvnieuwk nvnieuwk nvnieuwk left review comments

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
@maxulysse @nf-core-bot @FriederikeHanssen @nvnieuwk
0