Examples
Worked examples
- Is an instance
A genomics paper distributing its analysis as a Snakemake workflow with a `--use-conda` flag.
- Is an instance
A Snakemake pipeline executed locally for development and on Slurm for production.
Counter-examples
Looks similar, but isn't
- Not an instance
A pure CWL pipeline (different language).
- Not an instance
A bash script with no DAG inference.
Editorial commentary
Snakemake is widely used in bioinformatics for its declarative-yet-familiar Python syntax. It integrates with conda environments and container images, supports cluster and cloud execution, and produces provenance metadata. The 'concept' qualifier marks this entry as covering the methodological pattern rather than tracking implementation releases.
References
- Koster, Rahmann, 'Snakemake — a scalable bioinformatics workflow engine' (Bioinformatics, 2012); Molder et al., 'Sustainable data analysis with Snakemake' (F1000Research, 2021).
Also known as
Snakemake
Machine-readable encodings
Use in your systems
xml
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vocab-term="Snakemake (concept)"
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