Snakemake: pass command line arguments to scripts - snakemake

Question

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}"

Answer 1

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).

Answer 2

could you do something as simple an if statement to get parameters from snakemake or command line
that is
if snakemake in globals():
get parameters from snakemake
else:
get code some other way

Answer 3

Sounds like what you need is use of argparse in your python script. Here is an example, in which python script accepts arguments via commandline:
Python script example.py
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--infile", help="Filepath")
parser.add_argument("-o", "--outfile", help="Filepath")
args = parser.parse_args()
infilepath = args.infile
outfilepath = args.outfile
# blah blah code
Snakefile
rule xx:
input: "in.txt"
output: "out.txt"
shell: "python example.py -i {input} -o {output}"
PS - When I'm lazy, I just use Fire library instead of argparse. Fire easily exposes functions/classes to commandline with few lines of code.