I am not quite sure right now what the best way of doing it is in Snakemake, and since this might be relevant for many users, I thought I quickly ask here. I have two issues that both relate to how to maximize flexibility in the Snakemake universe:
If I use --cores, the (maximum) number of cores is specified. How do I best specify in my rules that this number should be used, how do I refer to it? So far, I specified a number explicitly (e.g., 1 for non-parallelizable and a fixed number like 8 for parallelizable ones), but this is not ideal and unflexible in fact.
Maybe I did something wrong but how do I correctly invoke the -configfile argument? If I use it to specify a valid config file, Snakemake complains about missing values in the "config" variable. I was expecting a different behaviour, namely that I have access to the "config" array if either --configfile is specified (which also overrides any "configfile:" statement ) or if a config file is specified via "configfile:". Only the latter seems to work?
Maybe this can be clarified in the documentation...