Problem description

This is an issues that we encountered when working on MOF-Search.

Snakefmt seems to be unable to parse correctly lambda functions used in the threads: section of rule definitions, due to which it then introduces line breaks in a way that invalidates the original Snakefile.

Example

Original Snakefile

rule decompress_and_run_cobs:
    output: "test"
    threads: lambda wildcards, input: get_number_of_COBS_threads(wildcards, input, predefined_cobs_threads, streaming)
    shell:
        """
        touch {output}
        """

Reformated Snakefile

If I run snakefmt Snakefile, I end up with the following Snakefile:

rule decompress_and_run_cobs:
    output:
        "test",
    threads: lambda wildcards, input: get_number_of_COBS_threads(
    wildcards, input, predefined_cobs_threads, streaming
)
    shell:
        """
        touch {output}
        """

Parsing errors

After which Snakemake fails with the following error:

$ snakemake -j1
SyntaxError in file /private/tmp/~20231128150941/Snakefile, line 5:
Unexpected keyword wildcards in rule definition (Snakefile, line 5)

And Snakefmt cannot be rerun either.

$ snakefmt  Snakefile 
snakefmt.exceptions.InvalidParameterSyntax: 4lambda wildcards , input: get_number_of_COBS_threads(

Version

$ snakefmt --version
snakefmt, version 0.8.5