feat: CLIN-3267 Bump version to 2.1.0

Bump the version with the following command: nf-core bump-version "v2.1.0dev"

I manually corrected the example commands in the README.md and USAGE.md documentation. I also manually updated CHANGELOG.md.

I run the linter and did not see any new warning caused by the changes.

PR checklist

[x] 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
[x] Make sure your code lints (nf-core 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>).
[x] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] Reference Data Documentation in docs/reference_data.md is updated.
[x] CHANGELOG.md is updated.
[x] README.md is updated (including new tool citations and authors/contributors).