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

Make validation of ontology terms optional #386

Merged
merged 3 commits into from
Jul 16, 2024
Merged

Make validation of ontology terms optional #386

merged 3 commits into from
Jul 16, 2024

Conversation

wfondrie
Copy link

@wfondrie wfondrie commented Jul 12, 2024 •
edited
Loading

This PR is our hotfix to address #385 by adding the validate_ontologies parameter. When false the SAMPLESHEET_CHECK process will only parse the SDRF file, but will not perform validation.

I'm sure there is a more elegant solution, but I thought this might be helpful as a starting point. Please feel free to ignore if it doesn't go in the right direction.

I'm also happy to add a test if someone could point me in the right direction 😉.

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/quantms branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

@github-actions GitHub Actions
Copy link

github-actions bot commented Jul 13, 2024 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d609e56

+| ✅ 292 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-13 07:43:04

@ypriverol ypriverol merged commit 687fd47 into bigbio:dev Jul 16, 2024
17 of 18 checks passed
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
2 participants
@wfondrie @ypriverol