Use wildcard in python shell rule

Question

I would like to do something like the following in Snakemake:

rule RULE:
  input: ...
  output: "{tool}/{file}"
  shell: lambda wildcards: command_for_tool[wildcards.tool]

possibly with the shell command wrapped in a format(.., file=wildcards.file) to expand the {file} that will be inside the command_for_tool.

Currently I can do this using a run: calling shell(..), but I can't use this because I'm benchmarking the memory usage of the rule and going via python adds 30+MB overhead.

It is possible to use some python code inside the shell: rule that returns a string, but in this case I cannot figure out how to use the wildcards.

It is also possible to use wildcards directly in a string value, where they will be substituted automatically, but this doesn't allow for the map-lookup I need.

Is there a clean solution to this? (Currently I'm trying to work around it using params:.) To me it seems like an omission/inconsistency in how snakemake works.

dariober · Accepted Answer · 2022-04-19 17:39:53Z

1

Using your own suggestion, a solution using params seems quite clean:

rule RULE:
    input:
        'in.txt',
    output:
        '{foo}.txt',
    params:
        cmd= lambda wc: command_for_tool[wc.foo],
    shell:
        """
        {params.cmd} 
        """

although I can see that for consistency with the input and params directive, also shell: lambda wildcards: command_for_tool[wildcards.tool] should work.

answered Apr 19, 2022 at 17:39

dariober

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1 Comment

Ragnar Over a year ago

Yes, this is basically what I have now, but note that the shell: "{params.cmd}" does not do recursive expansion, so you have to manually expand (with .format()) wildcards/variables that are part of the command line to be invoked.

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