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

Add nf-test skeleton #366

Open
wants to merge 6 commits into
base: dev
Choose a base branch
from
Open

Add nf-test skeleton #366

wants to merge 6 commits into from

Conversation

jfy133
Copy link
Member

@jfy133 jfy133 commented Apr 24, 2024

Replaces classic workflow with nf-tests (third attempt)

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/funcscan 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>).
  • 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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Apr 24, 2024 •
edited

nf-core lint overall result: Failed ❌

Posted for pipeline commit 8d909fb

+| ✅ 232 tests passed       |+
#| ❔   1 tests were ignored |#
-| ❌   2 tests failed       |-

❌ Test failures:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-05-08 13:31:15

@Darcy220606
Copy link
Contributor

Thank you @jfy133 !! Now lets get this done 💯

jfy133
jfy133 commented May 23, 2024
View reviewed changes
Copy link
Member Author

@jfy133 jfy133 left a comment

Choose a reason for hiding this comment

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

Just having a quick look - @jasmezz is there a reason why you're having indpeendent snapshots for every single file?

Why not snapshot (file1, file2, file3).match etc? If not all in one snapshot, you could at least group by tool?

@jasmezz
Copy link
Collaborator

jasmezz commented May 23, 2024

Yes, good question: I tried to do so, but the syntax from modules does not work on pipeline level for some reason. If you like it more compact, I will check how other pipelines do it.

@jasmezz
Copy link
Collaborator

jasmezz commented May 23, 2024

If not all in one snapshot, you could at least group by tool?

Also, they are grouped by tool at the moment. 🧐

@jfy133
Copy link
Member Author

jfy133 commented May 23, 2024

If not all in one snapshot, you could at least group by tool?

Also, they are grouped by tool at the moment. 🧐

I mean one .match per tool.

Check createtaxdb for s pipeline example

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
3 participants
@jfy133 @Darcy220606 @jasmezz