Add Binette

[prototaxites]

Add binette module for metagenome bin refinement. Unfortunate test depends on the large CheckM2 database...

@ochkalova I only realised as I made this PR you have a branch for Binette - happy to collaborate/work on your branch if you prefer!

PR checklist

Closes #XXX

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[ochkalova]

Thank you very much for doing this module! I never got to finishing it 😅

I left one request for an additional input arg.

Also, in my branch there is a 1.1 Mb test dataset that allows to make a test run without real CheckM2 DB. It still not super quick and requires a couple of minutes to finish, but I think it's better than downloading full CheckM2 DB... There is 2 tests for 2 options of input_type, I think we can only keep one of them.

The peculiarity here is to push this test data to nf-tests (that's why I never finished this module)

If you have capacity to it and update the test, would be great.

[ochkalova]

Is it a nf-core standard to compress fasta? I don't know if gz files are convenient for a regular user 🤔

[prototaxites]

It's a general nf-core recommendation to gzip files (https://nf-co.re/docs/specifications/components/modules/general#compression-of-input-and-output-files), but perhaps more importantly all the other nf-core binning modules also write gzipped fasta so its consistent for downstream use.

[prototaxites]

Hi @ochkalova, I have uploaded the test db to the repo but will no longer be able to work on this PR as I'm starting my paternity leave.

Happy for you to finish this up as you want, if you have time. Otherwise I'll pick this up when I'm back!

[ochkalova]

Hi @prototaxites! Wow, great news! 🐤
Ok, I'll try to finish this myself. Let's see what happens faster 😄