Conda envs: smaller YAML files
I would like to propose to have smaller conda
env. YAML files instead of the big monolithic per-step files being currently used.
According to snakemake
's documentation the conda
environments should be
as finegrained as possible to improve transparency and maintainability.
In many cases, it makes sense to have per-rule or per-tool YAML files, e.g. for MEGAHIT
or metaSPAdes
.
This could be discussed and decided for each step and rule to avoid installation of the same tools in different environments.