Perhaps the easiest way to do this would be to

1) replace all the stuff that is snakemake-specific with syntactically valid placeholders,
2) then run yapf on the modified file
3) then re-insert the snakemake specific stuff...

So that the below

rule get_gene_expression:
    input:
        expression_matrix
    output:
        "data/expression/series.csv"
    run:
        expression_matrix = pd.read_table(input[0])
        expression_series = expression_matrix.sum(1).sort_values(ascending=False)
        expression_series.to_csv(output[0], sep=" ")

becomes

for i in [1]: # snakemake
    for j in [2]: # snakemake
        expression_matrix = pd.read_table(input[0])
        expression_series = expression_matrix.sum(1).sort_values(ascending=False)
        expression_series.to_csv(output[0], sep=" ")

which you then can run yapf on. After yapf is run, the placeholder for i in [1] #snakemake is replaced with rule get_gene_expression:, for i in [2] #snakemake is replaced with ``` input:
expression_matrix
output:
"data/expression/series.csv"
run:

Just throwing it out there for criticism. It is very, very hackish, but seems like the minimally intrusive way of using yapf with snakefiles.

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