When using external software, create a CLI that uses Snakemake rules structured accoding to the following suggestions:
ctb blog
https://github.com/dahak-metagenomics/dahak
https://dahak-metagenomics.github.io/dahak-taco/
https://github.com/dahak-metagenomics/taco-simple
https://dahak-metagenomics.github.io/dahak-taco/DevWorkflows/