Yeah, this might be a better way to do it :)
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Botond Sipos
Tutorial: How to make your snakefiles self-documenting
I wrote a gist about how to make snakefiles self-documenting:
# 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.
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Ram
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Botond Sipos
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written
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Botond Sipos
2 answers
Thanks for posting. This can also be accomplished using native snakemake's objects, workflow and rule with docstring.
rule help:
"""
Print list of all targets with help.
"""
run:
for rule in workflow.rules:
print( rule.name )
print( rule.docstring )
rule do_something:
"""
Do something.
"""
run:
pass
You can then write a function to prettify the outputs.
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WouterDeCoster
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Eric Lim
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Eric Lim
Not sure if this is a newly added functionality, but I just realized one can simply do snakemake -l or snakemake --lt to display docstrings for each rule.
This is better than what I've been doing:
rule print_help:
"""Print help menu.
"""
run:
tbl = PrettyTable(['Rules', 'Description'])
tbl.align = 'l'
for rule in workflow.rules:
if not rule.name.startswith('_'):
tbl.add_row([rule.name, rule.docstring.splitlines()[0]])
print(tbl)
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Can you replace the URL redirector with a real URL? Otherwise we have no idea where that is going to take you.
Sure :)
I already did it.