Template update v2.0.1

[ggabernet]

• Update to nf-core tools template v2.0.1

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/bcellmagic branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• 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).

[ggabernet]

This is a huge PR again, to ease a bit the review, I'd like to say that modifications to R and python scripts that come shipped with the pipeline are strictly only to fix trailing spaces and indentation 4 spaces formatting, in accordance to the new editorconfig settings

[ggabernet]

The rest of the files have also only been strictly modified to adhere to the new template.

[FriederikeHanssen]

Phew that is a huge template update 🙈 Looks awesome!

[ggabernet]

Thanks a lot for your review @FriederikeHanssen , just fixed all your points!