An example of running through the entire Snakemake workflow

[adam2392]

Describe the problem

To provide documentation on how the entire workflow runs to go from .dcms to the output BIDS files and visualization engine, an example file is needed with screenshots where applicable.

Describe your solution

An example_workflow.rst file that sits in docs/ that walks through w/ an open-source set of dicoms.

Describe possible alternatives

Alternatively, rules.rst file that autodocs the Snakemake rule docstrings (idk how to do this though).

Additional context

See https://github.com/sequana/sequana which has some nice sphinx-gneerated docs from the snakemake rules. We can try to borrow the sphinx-ext code there.