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

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merged 7 commits into from
Jan 22, 2024
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Joon-Klaps
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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
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@jfy133 jfy133 left a comment

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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
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2 participants