First of all, I might have the wrong approach to this. I have a Snakemake pipeline that I used to run multiple types of simulations, and then run a program on these simulations. Depending on the type of simulation I run, a different set of parameters has to be used. For example, if I want the simulation that I called Ne over PI, I want Snakemake to use the following parameters set: N = [100, 1000] PI = [0.1, O.5] s = [0] For other simulations, I want these variable to take other values. What I would like to do, to keep it simple and easy to use, is to have a config file for each simulation, such as config_Ne_over_PI.yaml containing the parameters I described above. Therefore, when I call snakemake Ne_over_PI.results, my Snakefile should run the corresponding rule, and set the configfile to config_Ne_over_PI.yaml. But it seems that Snakemake is not able to decide between multiple config files depending on a condition ? Continue reading...
