Add BIDS support to the main workflow

[tsalo]

Our current plan for the workflow is to make it non-BIDS-specific (i.e., generic inputs and outputs), but we do want to support BIDS as an option.

Detailed Description

We will want to (1) add a --bids flag to the workflow, (2) add functions to ingest BIDS data and metadata, and (3) add the ability to generate BIDS-compatible derivatives. Thankfully, all three elements should be pretty straightforward, as confound timeseries are well established in fMRIPrep.

Context / Motivation

This will make it easier to apply phys2denoise in conjunction with other BIDS Apps. We can even make it easier to merge our outputs with fMRIPrep outputs so users don't need to do any additional work to get physio confounds.

Possible Implementation