Update more nf-core modules

[dialvarezs]

This PR updates all remaining nf-core modules, with the exception of porechop-abi, which is being updated in PR #854.

Aside from updating input channels where neccessary, the main changes are:

• In the ancient DNA subworkflow, the VCF index is now obtained directly from BCFTOOLS_VIEW instead of being generated in a separate indexing step.
• The test_single_end profile now downloads the full geNomad database. The reduced version we were using is not compatible with the current geNomad version. As an improvement, we could consider creating an updated mini geNomad database.

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).

[prototaxites]

Looks great, thanks @dialvarezs! Always happy for the removal of extraneous processes where possible 😎

re: the genomad db, I think there are instructions on the GitHub repo in an issue to create a smaller test DB. So we could look there to try and sort it.