How to run a one-time 'setup' step for amrfinder in snakemake using conda
There are two approaches you can take:


There's a --conda-create-envs-only option that you can use to exit after creating the envs. You should get information about where the envs are so you can run amrfinder -u.
Add a new rule called "amr_setup" or something like that that runs:


. 

amrfinder -u
touch amrfinder.setup


Then put amrfinder.setup into your snakemake workflow as an input file into the amr_finder_plus rule. Either of these will work