Apply template update for nf-core/tools version 3.2.0

[Daniel-VM]

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/bacass 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).

PR description

This PR updates the nf-core tools to version 3.2.0.

Major Changes

Implemented the latest template update.
Fixed lint warnings by:

• Cleaning up TODOs.
• Restructuring local module folders.
• Renaming and improving process names for consistency.

[famosab]

Looks good small questions :)

[Daniel-VM]

Thanks @famosab 🙌🏾

[famosab]

I think you should be good to go now if your tests pass aswell :)