Improve documentation

[fevac]

Description of feature

Improve and update official documentation. In particular:

• General review and update
• Add directory structure section (like https://nf-co.re/sarek/3.2.2/output#directory-structure)
• Update and improve output files description to help interpretation. Make clear which filtering is performed where (e.g. FusionInspector)
• Add the default options for each tool
  For inspiration:
• https://nf-co.re/rnaseq/
• https://nf-co.re/sarek

[rannick]

Add explanation for nan in megafusion when fusion is added by fusioninspector and was not identified by the tools/present in fusionreport

[rannick]

Closed in #396