I'm currently building my NGS pipeline using Snakemake and have an issue regarding the loading of R libraries. Several of the scripts, that my rules call, require the loading of R libraries. As I found no way of globally loading them, they are loaded inside of the R scripts, which of course is redundant computing time when I'm running the same set of rules on several individual input files. 
Is there a way to keep one R session for the execution of several rules and load all required libraries priorly?
Cheers,
zuup
I'm afraid not. This has performance reasons on (a) local systems (circumventing the Python GIL) and (b) cluster systems (scheduling to separate nodes).
Even if there was a solution on local machines, it would need to take care that no sessions are shared between parallel jobs. If you really need to safe that time, I suggest to merge those scripts.
Globally load R libraries in Snakemake