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snakemake

Snakemake: pass command line arguments to scripts

I am using some python scripts with snakemake to automate the workflow. These scripts take in command line arguments and, while I could replace them with snakemake.input[0], snakemake.output[0], etc, I am reluctant to do so since I'd also like to be able to use them outside of snakemake.

One natural way to solve this problem -- what I have been doing -- is to run them as a shell and not a script. However, when I do this the dependency graph is broken; I update my script and the DAG doesn't think anything needs to be re-run.

Is there a way to pass command line arguments to scripts but still run them as a script?

Edit: an example

My python script

import argparse

parser = argparse.ArgumentParser()
parser.add_argument("-o", type=str)
args = parser.parse_args()

with open(args.o, "w") as file:
    file.write("My file output")

My Snakefile

rule some_rule:
    output: "some_file_name.txt"
    shell: "python my_script.py -o {output}"
Solution

  • Based on comment from @troy-comi, I've been doing the following which -- while a bit of a hack -- does exactly what I want. I define the script as an input to the snakemake rule, which actually can help readability as well. A typical rule (this is not a full MWE) might look like

    rule some_rule:
    input:
        files=expand("path_to_files/f", f=config["my_files"]),
        script="scripts/do_something.py"
    output: "path/to/my/output.txt"
    shell: "python {input.script} -i {input.files} -o {output}"

    when I modify the scripts, it triggers a re-run; it's readable; and it doesn't require me to insert snakemake.output[0] in my python scripts (making them hard to recycle outside this workflow).