Update CheckM2

[dialvarezs]

• Update CheckM2 to v1.1.0
• Update default CheckM2 database to the latest (v3).

Closes #773.

PR checklist

• 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 pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[jfy133]

Thank you for this @dialvarezs !

Looks good only two comments:

• docs/output.md needs updating
• given the file name change, does anything downstream need to be updated to accommodate this (I'm thinking bin_summary.tsv)

[dialvarezs]

I updated output, and no, nothing changes downstream, because the file is the same as before, only renamed.

[jfy133]

@amizeranschi is going to do a mega test of the branch (as he has a lot of interest in this as busco is underperforming on a huge dataset), and will report back - if he says he is happy with it we will merge in and do a patch release :)

[amizeranschi]

This code worked fine for me with 300+ large metagenomic samples. CheckM2 seems great, BTW. It might even be worth it to set it as default, instead of BUSCO.