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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