overhaul documentation website

[kelly-sovacool]

Lots of TODOs to replace and details to fill in.

[slsevilla]

Not sure where to put this, but I think it mainly needs to be written clearly in the docs, so I'm putting it here.

We'll need to think about the difference between "input" and "control" in the metadata file and may want to assign a different name for each. Since we could have IgG instead of "input" this is can be confusing what this column is defining. I can trace the "input" param to macs2 -c, which is the 'control' option, making it even more confusing.