Update Docs & Consistency checks

[apeltzer]

Description of feature

Docs should be updated and consistency checked to match pipeline

[atrigila]

I am going to add here the changes that we could do related to style and syntax according to the new specifications.

Major:

• There are instances of params being used inside subworkflows or modules. They should be replaced by their corresponding channels.
• Params should be defined in the pipeline initialisation workflow. This workflow should emit channels that can be passed to the main smrnaseq workflow
• Params cannot be used outside the entry workflow

Minor:

• Apply nf-core naming conventions for local modules/subworkflows
• Input channel name should signify structure with the input object type
• Each input and output channel should have a comment describing the output structure of the channel