Updates of markdown files and default values in schema

[mazzalab]

Small updates to markdown and prettied files.
Local linting works with only a few warnings, but actions fail with odd errors of mismatches of images with the template.

PR checklist

• This comment contains a description of changes (with reason).
• 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>).
• 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).

[mashehu]

@nf-core-bot fix linting

[mashehu]

hi, hope it is okay, that I had a quick look at this, I know that you just started this, but I thought since I am already here because of the linting, I can give some small and hopefully helpful comments

[mashehu]

@nf-core-bot fix linting