v0.3.1-alpha: something wrong with conda envs

[ptrebert]

Looking at this reporting for the conda setup suggests that there are some mangled paths in the snakefiles:

Snakemake best practice is workflow/envs

[mir-cat]

I can look into this, but this doesn't happen for me, wither on my local machine or when I setup the environments on Hilbert. For me, the setup realizes that workflow/envs/env_cl.yaml and workflow/rules/../envs/env_cl.yaml are the same and only has one env creation step.