Readability

With Snakemake, data analysis workflows are defined via an easy to read, adaptable, yet powerful specification language on top of Python. Each rule describes a step in an analysis defining how to obtain output files from input files. Dependencies between rules are determined automatically.

Portability

By integration with the Conda package manager and container virtualization , all software dependencies of each workflow step are automatically deployed upon execution.

Modularization

Rapidly implement analysis steps via direct script and jupyter notebook integration. Easily create and employ re-usable tool wrappers and split your data analysis into well-separated modules.

configfile: "config.yaml"
rule all:
input:
expand( "plots/{country}.hist.pdf",
country=config["countries"]
 )
rule select_by_country:
input:
"data/worldcitiespop.csv" output:
"by-country/{country}.csv" conda:
"envs/xsv.yaml" shell:
"xsv search -s Country '{wildcards.country}' "
"{input} > {output}"
rule plot_histogram: input: "by-country/{country}.csv" output: "plots/{country}.hist.svg" container: "docker://faizanbashir/python-datascience:3.6" script: "scripts/plot-hist.py"
rule convert_to_pdf: input: "{prefix}.svg" output: "{prefix}.pdf" wrapper: "0.47.0/utils/cairosvg"

Transparency

Automatic, interactive, self-contained reports ensure full transparency from results down to used steps, parameters, code, and software.

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Scalability

Workflows scale seamlessly from single to multicore, clusters or the cloud, without modification of the workflow definition and automatic avoidance of redundant computations.

workstation

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compute server

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cluster

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grid computing

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cloud computing

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