big picture: turning this into a command line tool

it would be great if we could write a script that automatically converts the options in the config file into command line arguments

so that the pipeline could be called as a tool from the command line

there have been some attempts by snakemake users to try this type of thing (see snakepipes, etc), so maybe we should take a look at those to see if we could try to adapt them for us

Start by reviewing how the pipeline's config-file options are defined and passed through the existing Snakemake workflow. Compare the SnakePipes approaches mentioned in the issue, then define how the conversion should expose those options as command-line arguments and how a completed command-line invocation should work.

Written by the indexing model from the issue text.