Write usage documentation

[Jakob37]

First outline:

• Introduction
  • Conceptual overview of the purpose of the pipeline
  • Conceptual introduction to the running modes
• Running it
  • How to run it locally
  • Stub run
• How to deploy it
• Inputs
  • The samplesheet
  • Types of input data (i.e. FASTQ, BAM, VCF?)
  • Annotation files
  • Containers
• Profiles
  • Briefly outline the conceptual intent of each
  • High-level outline of the processing steps
  • What software are executed along each path
  • What annotation files are needed
• Software
  • A list of all included software with versions

Steps:

• [ ] Write a rough draft
• [ ] Write a preliminary first outline
• [ ] Check for feedbacks
• [ ] Look how it should be deployed. In a repo-yaml to build to read the docs?
• [ ] Write the yaml
• [ ] Make it deploy to readthedocs