Whenever module names are unrecognized (Keys from the species_configs), python and snakemake silently continues to execute, which in most cases will lead to snakemake missing input file errors. These types of errors are NOT informative in regards to Module names being unrecognized. The same thing goes for keywords (such as {database} and {assembly}).
Where reasonable, add simple checks and warning messages, to lead the user/developper on the right track. I believe that most checks can be added in the helper_functions.py script
Whenever module names are unrecognized (Keys from the species_configs), python and snakemake silently continues to execute, which in most cases will lead to snakemake missing input file errors. These types of errors are NOT informative in regards to Module names being unrecognized. The same thing goes for keywords (such as
{database}and{assembly}).Where reasonable, add simple checks and warning messages, to lead the user/developper on the right track. I believe that most checks can be added in the helper_functions.py script