Flying with Snakemake include keyword.
I wish to see what include does on multiple config files.
... wish granted.
For larger, reusable parts that shall be integrated into a common workflow, it is recommended to write small Snakefiles and include them into a main Snakefile via the include statement. In such a setup, all rules share a common config file.
- https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html
- I guess the "In such a setup, all rules share a common config file." part is only a suggestion.