combine_flow not in the documentation

[mdesco]

We need to mention our combine_flow in the documentation.
The philoshophy is:

• tree_for_* to prepare the input tree for a flow
• run the flow
• run the qc
• tree, flow, qc, repeat

@arnaudbore @zinelya Lets talk about this in person one day. I realize helping Maggie that this is not super clear for a new user.