I have folders upon folders of snakefiles for each of my projects.

I am usually in the base folder of my current project calling snakefiles in subfolders.

Example of my last invocation:

endrebak@havpryd ~/c/programmable_epigenetics> snakemake --snakefile snakefiles/csaw/graph_filter_parameters.snakefile -j 4.

Will read the docs of the functions you mentioned.

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