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Nextflow

Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows. It is a groovy-based language for expressing the entire workflow in a single script and also supports running scripts (via script/run/shell directive of Snakemake rule) from other languages such as R, bash and Python.

Available

Versions available on CSC's servers

  • Puhti: 21.10.6, 22.04.5, 22.10.1, 23.04.3, 24.01.0-edge.5903, 24.10.0
  • Mahti: 22.05.0-edge, 24.04.4
  • LUMI: 22.10.4

Pay attention to usage of Nextflow version

Please note that the nextflow version starting from 23.04.3 can only be used for pipelines built with DSL2. You can downgrade to lower versions for DSL1-compliant pipelines.

License

Nextflow is released under the Apache 2.0 license.

Usage

Nextflow on LUMI

To access CSC modules on LUMI, remember to first load the CSC module tree into use with

module use /appl/local/csc/modulefiles

Nextflow is activated by loading nextflow module:

module load nextflow

The default version is usually the latest. Choose the version of the Nextflow depending on the requirements of your own pipeline. It is recommended to load Nextflow module with a version, for the reproducibility point of view. To load nextflow module with a specific version:

module load nextflow/22.04.5

For usage help, use command:

nextflow -h

More detailed instructions can be found in CSC's Nextflow tutorial.

References

If you use Nextflow in your work, please cite:

Di Tommaso, P., Chatzou, M., Floden, E. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316–319 (2017). https://doi.org/10.1038/nbt.3820

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