Snakemake

Snakemake is a pythonic way of writing makefiles.

Snakemake works with distributions like anaconda to package and install dependencies. I recommend using Pyenv to keep things organized and separated out.

Installing

Pyenv

Main article: Pyenv

Regardless of what version or flavor of Python you wish to use, you can manage it using pyenv.

Quick start:

pyenv install anaconda3-5.0.1

pyenv global anaconda3-5.0.1

eval "$(pyenv init -)"

Check you have conda shimmed to your path:

which conda

Now install snakemake:

conda install -c bioconda snakemake

Conda

Main article: Conda

Snakemake is intended to be used in conjunction with Conda, which is a Python tool that enables installing software both inside and outside of the Python ecosystem.

conda install -c bioconda snakemake

This installs snakemake from the bioconda channel.

There is a much more extensive discussion of miniconda vs anaconda here: https://conda.io/docs/user-guide/install/download.html

Regular Python

If you don't need to install dependencies via conda, install snakemake via pip:

pip install snakemake

Using Snakemake

How It Works

The central idea behind Snakemake is to combine the flexibility and readability of Python's syntax with the concept of rules from Makefiles.

A rule in snakemake is a mapping from an input file to an output file.

rule plot:
    input:
        "raw/{dataset}.csv"
    output:
        "plots/{dataset}.pdf"
    shell:
        "somecommand {input} {output}"

Walkthrough Example

Walkthrough example with a non-trivial bioinformatics workflow called dahak-flot: Snakemake/DahakFlot

Strategies and Patterns

Stragies for designing Snakemake files and patterns for complex workflows: Snakemake/Patterns

Links

Projects

Snakemake documentation: https://snakemake.readthedocs.io/en/stable/

Snakemake for Bioconda documentation: https://bioconda.github.io/recipes/snakemake/README.html

Snakemake Biocontainer: https://quay.io/repository/biocontainers/snakemake

Snakemake wrappers for common bioinformatics components: https://snakemake-wrappers.readthedocs.io/en/stable/

Documentation

Rules: https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#targets

Setup/tutorial: https://snakemake.readthedocs.io/en/stable/tutorial/setup.html#step-1-installing-miniconda-3

Examples

A SingleCell RNASeq pre-processing pipeline built on snakemake: https://github.com/Hoohm/dropSeqPipe/blob/master/Snakefile

Amplicon trimming workflow using a short snakemake file: https://github.com/snakemake-workflows/accel-amplicon-trimming/blob/master/Snakefile

Both are listed on the snakemake workflows repo page: https://github.com/snakemake-workflows/docs