Snakemake is a workflow management system designed for scientific pipelines

Visit the Snakemake documentation site for installation guides and workflow references (opens in new tab)

• Created by Johannes Köster, first released in 2012
• Based on UNIX make - originally created in 1976 but still standard use
• Python based - “snake-make”
• Free and open source, available on Mac, Windows, Unix

Make is a command-line interface software tool that performs actions ordered by configured dependencies as defined in a configuration file called a makefile. It is commonly used for build automation to build executable code from source code. 

Snakemake Format

• Similar to writing shell scripts but snake files contains sets of rules
• Format is based on Python structure
• Snakemake reads from snakefile that defines the rules
• Snakefile rules have a target output
• Snakemake uses pattern matching to follow the inputs, outputs and commands contained in rules to reach final target output

Snakemake Core Idea

Instead of defining steps, you define rules that produce files

rule align:

input:
	"reads.fastq"

output:
	"aligned.bam"

shell:
	"bwa mem ref.fa {input} > {output}"

Snakemake builds a directed acyclic graph (DAG) automatically.

Fastq → Cutadapt → BWA → Sorted BAM → Freebayes → VCF