I am working on my PhD which requires plenty of different analyses. I collect the related analyses into different snakefiles in the same folders. My main reason for not having them in the same file is to keep the files small and easier to edit, understand and reason about.

Perhaps your setup would work if I created new folders for each snakefile, so that a/b.snakefile becomes a/b/Snakefile.

I guess you could ping https://github.com/johanneskoester and ask about his opinion.

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