add UPP

[lrauschning]

Adds a module for running MSA using UPP to nf-core. As there are some issues with the conda package for SEPP/UPP, this is drafted for now.

• [X] This comment contains a description of changes (with reason).
• [X] If you've fixed a bug or added code that should be tested, add tests!
• [X] If you've added a new tool - have you followed the module conventions in the contribution docs
• [X] Remove all TODO statements.
• [X] Emit the versions.yml file.
• [X] Follow the naming conventions.
• [X] Follow the parameters requirements.
• [X] Follow the input/output options guidelines.
• [X] Add a resource label
• [X 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

[SPPearce]

Within the maintainers team we've had a discussion recently, and we want to:

• keep the names of the meta maps as meta, meta2, meta3 etc across all modules for consistency.
• leave editing the meta maps to the workflow logic, not within modules.

[SPPearce]

@luisas, @lrauschning , I swapped to nf-test. The pytest was apparently using a bam file, which didn't seem right. Is there an appropriate test that could be make to work here, and get this module finished off?

[luisas]

We are currently not working on it anymore - we have decided to leave this one aside as it was giving us too many issues and we have other comparable aligners.

I would propose we close this one PR, @lrauschning what do you think?

[lrauschning]

Yeah, UPP was causing quite a few issues and I was never able to reliably get it packaged for conda (its packaged with SEPP and TIPP, and requires some file wrangling), so it got sidelined in favour of MAGUS. I don't have the time to work on that right now, so will close the PR – if anyone else wants to work on it, they can pull from the branch in my fork of nf-core/modules and open a new PR.