script reusability outside snakemake

[jordandekraker]

Currently all python scripts are interacted with using snakemake.inputs.x or snakemake.outputs.y. This makes them very annoying to use outside of a snakemake workflow, e.g., for one-time use or applying code to other projects. It would be nice to optionally use import argparse or import sys, getopt to parse these arguments instead at the top of each script.

[akhanf]

That's the tradeoff with easy development of workflow scripts in snakemake -- instead of trying to make the snakemake scripts callable from outside, I think the better approach for established functions could be to put them in their own importable module, and the snakemake script can call it. Also anything outside hippunfold could also import them if we package it up appropriately.

The module ( or modules if we organize them into multiple files) themselves could be in inside the hippunfold package and repo still too (sibling to the snakemake workflow files perhaps), to keep things together for maintenance and testing.