One single config file

[grexor]

Instead of having splicekit.config for specific splicekit setup, and config.yaml for having specific snakemake setup, join the two parameter files into a single yaml file, read by both snakemake and splicekit;

[grexor]

Perhaps a better alternative is to have two files, both in yaml:

a) snakemake.yaml, this file would include parameters directly relevant to the snakemake workflow
b) config.yaml, this file would include parameters specific to the experiment / dataset that is being processed

In this way we would keep general (that do not change much) parameters in the snakemake.yaml file, and dataset specific parameters (genome, etc) in the config.yaml file.