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Snakemake

Snakemake is a Python-based scientific workflow management system for creating scalable, portable, and reproducible workflows. It is one of the popular workflow managers within the bioinformatics community, but is not specific to bioinformatics. Like in Nextflow, Snakemake also supports running scripts (via script/run/shell directive of Snakemake rule) from other languages such as R, bash and Python.

Available

Versions available at CSC:

  • Puhti: 7.15.2, 7.17.1, 8.4.6

License

Snakemake is released under the MIT License.

Usage

Snakemake is activated by loading snakemake module as below:

module load snakemake

Example of loading snakemake module with a specific version:

module load snakemake/8.4.6

For usage help, use command:

snakemake --help

Please refer to our tutorial on running Snakemake workflow on Puhti for more details.

Installation

The latest version of snakemake (v8.4.6) was installed on Puhti using virtual environment via pip3. See a list of the python packages used in this module .

References

If you use Snakemake in your work, please cite:

Mölder, F., Jablonski, K.P., Letcher, B., Hall, M.B., Tomkins-Tinch, C.H., Sochat, V., Forster, J., Lee, S., Twardziok, S.O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., Nahnsen, S., Köster, J. Sustainable data analysis with Snakemake. F1000Research 2021, https://doi.org/10.12688/f1000research.29032.1.

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