Possible solution
Isolate all R code on specific files, the location can be accessed via config, for instance. Structure the code in a way that is possible to pass the Snakemake variables as arguments (silly example). Once the code is isolated it should be easier to stablish unit tests for all of them.
Issue R code is kept in the Snakemake files and directly take variables from it. For example, rule filter in
DE_pipeline. Snakemake
:Possible solution Isolate all R code on specific files, the location can be accessed via config, for instance. Structure the code in a way that is possible to pass the Snakemake variables as arguments (silly example). Once the code is isolated it should be easier to stablish unit tests for all of them.