add module for panaroo, fix pirate tests

[rpetit3]

PR checklist

Closes #1443

• 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

I opted for panaroo/run because panaroo has a few other sub-commands that might be added in the future. I also cleaned up some lingering comments in the PIRATE test main.nf

[rpetit3]

Pirate conda is failing with this:

 - ERROR: extract_feature_sequences.pl failed

Going to try pinning a specific build. Haha honestly didn't mean for this to turn into a new module and fix for old module!

[rpetit3]

Had to pin bioperl to 1.7.2. The containers are not affected by this due to having 1.7.2

[rpetit3]

Pirate issue is addressed here: #1094

[edmundmiller]

LGTM!