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

Kaiju version bump- nf-test -add stub #4781

Merged
merged 7 commits into from
Jan 22, 2024
Merged

Conversation

Joon-Klaps
Copy link
Contributor

PR checklist

kaiju modules:

  • bump-version
  • migrate to nf-test
  • add stub run

Kaiju2table was using *.fmi for the name database instead of names.dmp which resulted in taxonid's instead of taxon names in the output files.

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

@Joon-Klaps Joon-Klaps marked this pull request as ready for review January 20, 2024 18:57
@Joon-Klaps Joon-Klaps requested a review from ahvigil January 20, 2024 18:57
Copy link
Member

@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.

LGTM! Thanks @Joon-Klaps !

@Joon-Klaps Joon-Klaps added this pull request to the merge queue Jan 22, 2024
Merged via the queue into master with commit 3db5067 Jan 22, 2024
19 checks passed
@Joon-Klaps Joon-Klaps deleted the kaiju2table-dbname-fix branch January 22, 2024 11:34
jennylsmith pushed a commit to RSC-RP/modules that referenced this pull request Mar 20, 2024
* kaiju modules patch

* add kaiju nf-test and stub

* adding test & stub 4 kaiju2krona

* undo raven change

* kaiju2table & kaijumkfmi

* Add taxonomic profiling as a keyword in meta.yml
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
Status: Done
Development

Successfully merging this pull request may close these issues.

2 participants