How to add help function in a snakemake file

Question

[c.clarido]

Hello community,

How do you add help function in a snakemake file such that it will print a description of the workflow when you enter:

snakemake --snakefile Snakefile help

I tried the following: import argparse

parser = argparse.ArgumentParser(
        description='''ENTER DESCRIPTION HERE.''')
args = parser.parse_args()

rule invenU:
    input: ["/home/bnextgen/reads/bngsa_nietinfected_1.fastq","/home/bnextgen/reads/bngsa_nietinfected_2.fastq"]  
    output: ["/home/s1104230/output/iutr1.fastq", "/home/s1104230/output/iutr2.fastq"]
    script: "/home/s1104230/scripts/inven.py"
    # input: ["/home/s1104230/data/bngsa1_24M.txt","/home/s1104230/data/bngsa2_24M.txt"]  
    # output: ["/home/s1104230/output/iutr1.fastq", "/home/s1104230/output/iutr2.fastq"]
    # script: "/home/s1104230/scripts/inven.py"

I get the following error back:

Cedricks-MacBook-Pro:scripts cedrickagaser$ snakemake --snakefile Snakefile help
usage: snakemake [-h]
snakemake: error: unrecognized arguments: --snakefile Snakefile help
SystemExit in line 10 of /Users/cedrickagaser/Documents/bnextgen/scripts/Snakefile:
2
  File "/Users/cedrickagaser/Documents/bnextgen/scripts/Snakefile", line 10, in <module>
  File "/Users/cedrickagaser/miniconda3/lib/python3.6/argparse.py", line 1737, in parse_args
  File "/Users/cedrickagaser/miniconda3/lib/python3.6/argparse.py", line 2393, in error
  File "/Users/cedrickagaser/miniconda3/lib/python3.6/argparse.py", line 2380, in exit

the argeparse method works well with other python programs but with Snakefile not.

Answer 1

[dariober]

One option may be to print the help when a given configuration key is given, for example help:

snakemake --config help=1 -s snakefile.smk

Help for this script

USAGE

snamekemake -s snakefile.smk ...

I think this works nicely but it's a bit ugly to invoke help using --config help=1.

Alternatively, you could have a help rule that all it does is to print the help message. You then invoke help with:

snakemake -s snakefile.smk help

The problem with this solution is that the help message gets surrounded with the logs from the snakemake execution.

TL;DR Good question. It would be nice if snakemake had a dedicated option for doing this...

---

The snakefile.smk script:

import os

docstring= r"""
Help for this script

USAGE

snamekemake -s snakefile.smk ...
    """

if 'help' in config:
    print(docstring)
    os._exit(0)

rule all:
    input:
        'foo.txt'

rule help:
    run:
        print(docstring)

rule make_foo:
    output:
        'foo.txt'

[c.clarido]

Thank you, I added a rule where I "cat" the help description from a file and it works fine.

Answer 2

[Philipp Bayer]

Maybe this older tutorial and its answers can help you?