Refactoring of local modules for future release

[tillenglert]

Description of feature

The local modules could be refactored as suggested by @nvnieuwk. The structure of modules should adhere more to nf-core modules. Therefore each module will be in its own directory so instead of module.nf it will get module/main.nf. This will also give space to attach env files, and ymls for documentation and future release to nf-core modules.

Also stub test would be a great addition!