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

Fix validation for bruker files #316

Merged
merged 1 commit into from
Mar 26, 2024
Merged

Fix validation for bruker files #316

merged 1 commit into from
Mar 26, 2024

Conversation

jonasscheid
Copy link
Collaborator

@jonasscheid jonasscheid commented Mar 26, 2024 •
edited
Loading

file-path of nf-validation plugin only supports files, not the combination of files and directories like in the case of bruker .d. Need to default back to checking only the path. Fetching seems to work still.

Need to setup test cases asap --> #306

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/mhcquant 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 Mar 26, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅

Posted for pipeline commit 1261417

+| ✅ 200 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-26 14:13:24

@marissaDubbelaar
Copy link
Collaborator

LGTM but why it is possible to put a "-?" In the name? It that not weird for an extension?

@jonasscheid
Copy link
Collaborator Author

I have no clue, that was autogenerated by a template update. But this in now removed and we should be good to go with \\S+ : \\S matches any non-whitespace character

@jonasscheid jonasscheid merged commit e0f2cee into nf-core:dev Mar 26, 2024
7 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@marissaDubbelaar marissaDubbelaar marissaDubbelaar 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
@jonasscheid @marissaDubbelaar