OK, so I've played around with adding the different fontification for the minilanguage parts, and ... I really don't like it! :) I think the thing is, my brain is so used to a break in the string fontfication signaling the end of a string, so all my strings just look broken. Dunno, perhaps it's something I'd get used to.

To try this out yourself, you could do something like (changing font-lock-variable-name-face to whatever face you'd like):

(add-to-list 'snakemake-font-lock-keywords
             `("{[^}]+}" 0 font-lock-variable-name-face t))

What do others think?

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