How to perform simple string operations in snakemake output

Question

I am creating my first snakemake file, and I got to the point where I need to perform a simple string operation on the value of my output, so that my shell command works as expected:

rule sketch:
  input:
    'out/genomes.txt'
  output:
    'out/genomes.msh'
  shell:
    'mash sketch -l {input} -k 31 -s 100000 -o {output}'

I need to apply the split function to {output} so that only the name of the file up to the extension is used. I couldn't find anything in the docs or in related questions.

Answer 1

Best is to use params:

rule sketch:
    input:
        'out/genomes.txt'
    output:
        'out/genomes.msh'
    params:
        prefix=lambda wildcards, output: os.path.splitext(output[0])[0]
    shell:
        'mash sketch -l {input} -k 31 -s 100000 -o {params.prefix}'

It is always preferable to use params instead of using the run directive, because the run directive cannot be combined with conda environments.