Making Snakemake workflows into full-fledged command line tools since 1999.
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README.md

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Snakeparse

Making Snakemake workflows into full-fledged command line tools since 1999.

Warning: this project is under active development; the API will change!

Why Snakeparse?

  • I wanted a single command line utility that could organize and execute multiple Snakemake workflows
  • I wanted to have my workflow-specific arguments be parsed on the command line (ex. with argparse)
  • I wanted an API or library to configure how to group and organize the workflows, and how to display them on the command line.
  • I didn't want to write this library more than once.

Demo

Snakeparse Demo

Installation

Python 3.6 or higher is required.

Snakemake 4.4.0 or higher is required.

To clone the repository: git clone https://github.com/nh13/snakeparse.git.

To install locally: python setup.py install.

The command line utility can be run with snakeparse

Conda Recipe

See the recipe on Bioconda.

Documentation

See the following Documetnation

Testing

To run tests, run coverage run -m unittest discover -s src

To obtain test coverage, run codecov.

Snakeparse on the Command Line

To get started, run snakeparse --help.

More documentation is coming soon, but see the source API documentation in the meantime.

Example

  1. Using argparse and a custom method named snakeparser.
  2. Using argparse and a concrete sub-class of SnakeParser.

For more examples, see this link.

The example below is from (1).

Motivation

Consider this simple Snakemake file (snakefile) that has a required configuration option:

message = config['message']

rule all:
    input:
        'message.txt'

# A simple rule to write the message to the output
rule message:
    output: 'message.txt'
    shell: 'echo {message} > {output}'

You would need to run snakemake with the --config option:

snakemake --snakefile </path/to/snakefile> --config message='Hello World!'

If you forget to add the correct key/value pairs with the --config option, you'll get a KeyError exception, which is not user-friendly to non-programmers. At that point, you're out of luck to see all the various required and optional config key/value pairs without examining the snakefile (i.e. you want to see a help message). Have fun adding each configuration option one-by-one and gleaning their meaning. Even examining the source, there needs to be clear documentation within your snakefile for each argument for the user to examine. Why can't we just use argparse as we normally would for our command-line python scripts?

Furthermore, if you have multiple snakefiles, setting the --config key/value pairs can get quite painful, notwithstanding the fact you need to specify the path to the specific snakefile your interested in each time. Why can't we put all the snakefiles in one place, and have an easy way to specify which to run on the command line? So many other command-line tools do it (ex. bwa, samtools, fgbio, Picard), and even other workflow software do it (ex. dagr), why can't we do it?

This is why I wrote Snakeparse.

Setup

Source: examples/argparse/method/write_message.smk

Modify the above snakefile by prepending the following:

# Import the parser from snakeparse
from snakeparse.parser import argparser

def snakeparser(**kwargs):
    ''' The method that returns the parser with all arguments added. '''
    p = argparser(**kwargs)
    p.parser.add_argument('--message', help='The message.', required=True)
    return p

# Get the arguments from the config file; this should always succeed.
args = snakeparser().parse_config(config=config)

# NB: you could use `args.message` directly.
message = args.message

Execution

Snakeparse Command Line Execution

You can run the installed snakeparse utility as follows:

snakeparse --snakefile examples/argparse/method/write_message.smk -- --message 'Hello World!'

or

snakeparse --snakefile-globs examples/argparse/method/*smk -- WriteMessage --message 'Hello World!'

Programmatic Execution

config = SnakeParseConfig(snakefile_globs='~/examples/argparse/method/*smk')
SnakeParse(args=sys.argv[1:], config=config).run()

or alternatively SnakeParse accepts leading configuration arguments:

args = ['--snakefile-globs', '~/examples/argparse/method/*smk'] + sys.argv[1:]
SnakeParse(args=args, config=config).run()