This might be an issue with Black, but not sure.

Minimal example:

rule my_rule:
    input:
        data=(
            # a comment on the below
            "input_1.txt"
            if condition
            else "input_2.txt"
        )

Obviously, this is not good style, and the comment should go before the the data line anyway - which is what I'll do to fix this. However, it still should not break the formatting.

Error:

snakefmt.exceptions.InvalidPython: Black error:
Cannot parse: 2:0: EOF in multi-line statement

Python itself does not complain about this, and so I think neither should do the formatter, despite the bad style, and instead just simply move the comment up, as it does in similar situations without parenthesis.