Update documentation

[imendes93]

Closes #328

This PR does an overhaul of the documentation for splicing-pipelines-nf, which now is divided into the following parts:

• 1 - Pipeline description
  • 1.1 - Pipeline overview
  • 1.2 - Input
  • 1.3 - Default processes
  • 1.4 - Optional processes
  • 1.5 - Output
  • 2 - Options
  • 3 - Usage
    • 3.1 - Running with Docker or Singularity
    • 3.2 - Submitting run to CloudOS
    • 3.3 - Execution examples
  • 4 - Additional information
    • 4.1 - Quick start on Sumner
    • 4.2 - Additional documentation

[angarb]

Hi @imendes93 - I think this is looking awesome! One thing that might be a mental leap for users is how to go from a 'Quick Test' to running the pipeline locally. https://github.com/TheJacksonLaboratory/splicing-pipelines-nf/blob/update-docs-238/docs/run_locally.md

This is something I do not know! Do you need to make a local folder with all of your docs? How do you specify your config in the nextflow run line? Maybe it would help to give an example of running real data and how parameters are specified (because we do this a bit differently on Sumner with the main.pbs).