big picture: turning this into a command line tool

[aryarm]

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

[aryarm]

see #5 for a related issue about validation of config options

basically, we need something that will parse the config options as flags and arguments (probably argparse?). And then once we've parsed the arguments, we should perform validation steps to ensure that the user provided the correct input and then, before we even execute the pipeline, we should error out with informative messaging if they haven't.
That is what a command line tool does.