Generate command list as top-level running

[hyphaltip]

Running the tool with all-in-one options so that it generates a BASH / Makefile or script to run all the sub-pieces so that user does not have to write script to do all the steps.

Support "smart" restart options in the pipeline so that previously run steps are not re-done.

This seems like a solution for snakemake or makefiles instead of shell scripts....

[nextgenusfs]

yeah I wouldn't use a shell script (I do that locally for ease but too easy to break) -- but can do this in python as well I think instead of adding another dependency. although a makefile obviously wouldn't be a dependency -- I will be virtually no help with that....

To do in python we just need to parse the arguments correctly -- I've not looked at the overall current argparse structure to know if we can get all unique arguments into an argparse object? Then just need to filter for each tool for the function calls.