Nextflow

Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows.

• Nextflow
  • Available
  • License
  • Usage
  • References
  • More information

Available

Versions available on CSC's servers

• Puhti: 21.10.6, 22.04.5, 22.10.1, 23.04.3
• Mahti: 22.05.0-edge
• 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 as below:

module load nextflow

Example of loading 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

More information

• Nextflow documentation
• Running Nextflow on Puhti
• High-throughput Nextflow workflow using HyperQueue
• Contact CSC Service Desk for technical support

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Last update: November 7, 2023

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