Replace bash script coordination with snakemake workflow

[tomalrussell]

See https://snakemake.readthedocs.io

Is your feature request related to a problem? Please describe.
The current bash run.sh is fairly unfriendly to use: typically involves commenting/uncommenting pieces to run and debug, contains some repetition, shouldn't grow too much longer or more complicated.

Describe the solution you'd like
Rewrite run.sh as a Snakefile to run the workflow.

Describe alternatives you've considered
Leaving as-is; GNU Make; plenty of other workflow systems which generally look a bit heavier to get started with.

Additional context
nismod/smif#398 suggests snakemake as model-run scheduler - would be good to align if/when that goes ahead, this might be a good testing ground.