CODEWITHSUNDEEP
pythonsnakemake
Gerhardt Schmidt
Gerhardt Schmidt

Reputation: 83

Snakemake - How to produce multiple outputs from single input, multiple times with different seeds?

I am trying to create a snakemake rule that produces 3 output files for each given seed. I currently have the following:

SIM_OUTPUT = ["summary", "tripinfo", "vehroute"]
SEEDS = [1,2]
single_seed = 1
rule sumo_sim_1:
    input:
        config = "two-hours-ad-hoc.sumo.cfg"
    output:
        expand("xml/{file}.{seed}.xml", seed = single_seed, file=SIM_OUTPUT)
    shell:
        " sumo -c {input.config} --seed {single_seed}" 
        "--summary-output {output[0]} "
        "--tripinfo-output {output[1]} " 
        "--vehroute-output {output[2]} "

The above code works for a single seed, but I cant get/think of a way to work for multiple seeds.

Upvotes: -1

Views: 1349

Answers (1)

Maarten-vd-Sande
Maarten-vd-Sande

Reputation: 3701

First you need to change your rule to make use of your seed wildcard like so

rule sumo_sim_1:
    output:
        "xml/summary.{seed}.xml",
        "xml/tripinfo.{seed}.xml",
        "xml/vehroute.{seed}.xml",
    shell:
        " sumo -c {input.config} --seed {wildcards.seed} "
        "--summary-output {output[0]} "
        "--tripinfo-output {output[1]} " 
        "--vehroute-output {output[2]} "

And then your downstream rule(s) can just specify the seed necessary for their input, like so:

rule all:
    input:
        ["xml/summary.1.xml", "xml/summary.2.xml", "xml/tripinfo.1.xml", "xml/tripinfo.2.xml", "xml/vehroute.1.xml", "xml/vehroute.2.xml"]

Upvotes: 1

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