Parallel execution of a snakemake rule with same input and a range of values for a single parameter - snakemake

Question

I am transitioning a bash script to snakemake and I would like to parallelize a step I was previously handling with a for loop. The issue I am running into is that instead of running parallel processes, snakemake ends up trying to run one process with all parameters and fails.
My original bash script runs a program multiple times for a range of values of the parameter K.
for num in {1..3}
do
structure.py -K $num --input=fileprefix --output=fileprefix
done
There are multiple input files that start with fileprefix. And there are two main outputs per run, e.g. for K=1 they are fileprefix.1.meanP, fileprefix.1.meanQ. My config and snakemake files are as follows.
Config:
cat config.yaml
infile: fileprefix
K:
- 1
- 2
- 3
Snakemake:
configfile: 'config.yaml'
rule all:
input:
expand("output/{sample}.{K}.{ext}",
sample = config['infile'],
K = config['K'],
ext = ['meanQ', 'meanP'])
rule structure:
output:
"output/{sample}.{K}.meanQ",
"output/{sample}.{K}.meanP"
params:
prefix = config['infile'],
K = config['K']
threads: 3
shell:
"""
structure.py -K {params.K} \
--input=output/{params.prefix} \
--output=output/{params.prefix}
"""
This was executed with snakemake --cores 3. The problem persists when I only use one thread.
I expected the outputs described above for each value of K, but the run fails with this error:
RuleException:
CalledProcessError in line 84 of Snakefile:
Command ' set -euo pipefail; structure.py -K 1 2 3 --input=output/fileprefix \
--output=output/fileprefix ' returned non-zero exit status 2.
File "Snakefile", line 84, in __rule_Structure
File "snake/lib/python3.6/concurrent/futures/thread.py", line 56, in run
When I set K to a single value such as K = ['1'], everything works. So the problem seems to be that {params.K} is being expanded to all values of K when the shell command is executed. I started teaching myself snakemake today, and it works really well, but I'm hitting a brick wall with this.

Answer 1

You need to retrieve the argument for -K from the wildcards, not from the config file. The config file will simply return your list of possible values, it is a plain python dictionary.
configfile: 'config.yaml'
rule all:
input:
expand("output/{sample}.{K}.{ext}",
sample = config['infile'],
K = config['K'],
ext = ['meanQ', 'meanP'])
rule structure:
output:
"output/{sample}.{K}.meanQ",
"output/{sample}.{K}.meanP"
params:
prefix = config['invcf'],
K = config['K']
threads: 3
shell:
"structure.py -K {wildcards.K} "
"--input=output/{params.prefix} "
"--output=output/{params.prefix}"
Note that there are more things to improve here. For example, the rule structure does not define any input file, although it uses one.

Answer 2

There is an option now for parameter space exploration
https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#parameter-space-exploration