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Nextflow enables reproducible computational workflows

Nature Biotechnology volume 35, pages 316–319 (2017)Cite this article

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To the Editor:

The increasing complexity of readouts for omics analyses goes hand-in-hand with concerns about the reproducibility of experiments that analyze 'big data'1,2,3. When analyzing very large data sets, the main source of computational irreproducibility arises from a lack of good practice pertaining to software and database usage4,5,6. Small variations across computational platforms also contribute to computational irreproducibility by producing numerical instability7, which is especially relevant to high-performance computational (HPC) environments that are routinely used for omics analyses8. We present a solution to this instability named Nextflow, a workflow management system that uses Docker technology for the multi-scale handling of containerized computation.

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Figure 1: Nextflow enables stable analyses on different platforms.

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Acknowledgements

We wish to thank T. Ferrar and J. Cotter for manuscript revision and helpful comments, and R. Guigo for suggesting ENCODE applications. This project was supported by the Center for Genomic Regulation and the Spanish Plan Nacional and the Spanish Ministry of Economy and Competitiveness, 'Centro de Excelencia Severo Ochoa 2013-2017'. M.C. and E.W.F. were supported by the La Caixa Foundation. We acknowledge the support of the CERCA Programme/Generalitat de Catalunya.

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Author notes

  1. Paolo Di Tommaso, Maria Chatzou and Evan W Floden: These authors contributed equally to this work.

Authors and Affiliations

  1. Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain

    Paolo Di Tommaso, Maria Chatzou, Evan W Floden, Pablo Prieto Barja, Emilio Palumbo & Cedric Notredame

  2. Universitat Pompeu Fabra (UPF), Barcelona, Spain

    Maria Chatzou, Evan W Floden & Pablo Prieto Barja

Authors
  1. Paolo Di Tommaso
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  2. Maria Chatzou
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  3. Evan W Floden
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  4. Pablo Prieto Barja
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  6. Cedric Notredame
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Correspondence to Cedric Notredame.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Methods, Supplementary Table 1 and Supplementary Figures 1–3 (PDF 1448 kb)

Supplementary Code

Nextflow 0.22.0 Code (ZIP 2056 kb)

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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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