self_document.snake

# This snippet add the "self-documenting" feature to snakemake files. 
# It is inspired by the Makefile in https://github.com/audreyr/cookiecutter-pypackage

# Add the follwing to your snakefile or include: "self_document.snake"

import re
def generate_help(sfile):
    """Parse out target and help message from file."""
    handler = open(sfile, "r")
    for line in handler:
        match = re.match(r'^rule\s+([a-zA-Z_-]+):.*?## (.*)$$', line)
        if match:
            target, help = match.groups()
            print("%-20s %s" % (target, help))

rule help: ## print list of all targets with help
    input:
        workflow.included
    run:
        print("--------------------------------------------")
        [generate_help(sfile) for sfile in input]
        print("--------------------------------------------")

# Then simply add a comment to your rule line preceded by '##'. Invoking snakemake help will print all targets and their descriptions.