PR checklist

Closes #1772

• 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

Few things.

Hard-coded bioconda build number

I had to force the build number in relation to bioconda/bioconda-recipes#35314 Previous builds didn't not include the required database, and it being only ~500kb, I submitted a new build to include it.

bioconda::plasmidfinder=2.1.6=py310hdfd78af_1

Avoid name collisions

PlasmidFinder does not include a --prefix parameter, so I manually move the output files to include the $prefix this should help avoid downstream name collisions.