Allow YAML-based config file with input arguments from/for workflow

[tsalo]

We want to add the ability to ingest and write out YAML-based config files when running the workflow.

Stems from #17 (comment) and GatherTown convo.

Detailed Description

Running the workflow will automatically write out a YAML file to the output directory with all arguments used in the original call. Users will also be able to feed in a --config-file argument that will take parameters from a YAML file and use them in the workflow call. Any manually specified arguments will override ones in the YAML file (perhaps with a warning?).

Context / Motivation

This will make it easier to re-run the workflow, as well as to run the workflow on many participants with limited variable hard-coding.

Possible Implementation