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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.

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    Do you need to specify the SIM_OUTPUT part through expand? With three files you could easily name and specify them individually in the output section (summary_output = "xml/summary.{seed}.xml" etc.) Commented Apr 4, 2022 at 12:13

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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"]
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