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.

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

Added test_nothing nf-test and updated CI #620

Open
wants to merge 14 commits into
base: dev
Choose a base branch
from

Conversation

CarsonJM
Copy link
Contributor

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/mag 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).

Copy link

github-actions bot commented May 23, 2024

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5619352

+| ✅ 307 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-23 19:25:13

@prototaxites
Copy link
Contributor

Not knowing much (yet) about nf-test - I think this looks great!

I had a poke around in the failing tests - here, the kreport test fails because the test reads the mag conf/modules.conf and sets the prefix as ext.prefix = { "${meta.id}_kreport" }, whereas the test snapshot expects the output file to just be called ${meta.id}.txt. I suspect this could be a problem for any test where we're manually setting a prefix and adding custom strings to it which aren't hard-coded in the process itself. Off the top of my head this may cause problems with the read QC filtering, phiX removal, etc. as these add prefixes like "_host_removed" to separate out fastq files which otherwise would have the same names.

@CarsonJM
Copy link
Contributor Author

Thanks for taking a look at this @prototaxites! I'll look at the module configs today and see which ones need to be changed, I think this is something we can override in an nf-test config 👌

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants