How our pipelines are documented

To keep documentation up to date, we save it close to the respective code:

• Each pipeline folder in this repo contains a README.md with its description.
• Protocols are documented by adding "#DOC its purpose" below the "#MOLGENIS ..." directive.
• The parameters.csv file contains a 'description column' for each of the parameters.
• R-scripts: The main script always starts with "#!/usr/bin/env Rscript" so that it can be started from command line.
• Second line in script: "#DOC my purpose is...".
• Calling it from the command line without parameters provides help:
• Example how to run script
• Purpose of script
• A list of parameters with shorthand and description, e.g.:
  • --parameter -p indicates ...

TODO: auto-generate documentation of analysis runs

Additional advantage is that the Compute software can auto-generate documentation of an analysis we've performed by combining

• The pipeline's README.md
• The workflow.csv (graph with 'dot' as we already have)
• The #DOC's for each of the protocols in workflow.csv (each protocol once)
• A list of parameters and their values (with short description)