Document the Pipeline Functionality

[apeltzer]

For each configurable parameter, we should have documentation.

[jfy133]

Let me know once you're at a stage where the core pipeline steps are stable and I can start contributing to that.

[apeltzer]

Now :-D

I'll add the genotyping capabilities in the next release V2.1, as its not entirely clear to me what people are using anymore. I figured that EAGER1.X is running outdated methods there... so we should discuss that here: #40