use snakemake validation

[aryarm]

Snakemake can validate config files. It will be easier for people to use your pipeline if they know what its inputs are. Get on this

[aryarm]

this is becoming more and more relevant as the config files become more logic-heavy. it can be hard for the user to know what they must include when so many of the options are either dependent on each other or optional in some cases.
rather than specify and explain the complexities of the config files in words, it may simply be easier to let the user validate them each time. or maybe the best approach uses both. think about it