Documentation missing

In the pipeline results section there is no mention of the merged output, i.e. all.A.psi.tsv, all.A.cosi.tsv, etc. 

Also it would be nice if there is a small description of how the pipeline work. Maybe you can just add a link to this pdf from [ipsa-full](https://github.com/pervouchine/ipsa-full/blob/master/latex/sjpipeline.pdf). It helped me understand a bit better the output of the pipeline.