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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.

References

  1. Allison, D.B., Brown, A.W., George, B.J. & Kaiser, K.A. Nature 530, 27–29 (2016).

    Article  CAS  Google Scholar 

  2. Editorial. Nat. Methods 12, 1099 (2015).

  3. Editorial. Nat. Biotechnol. 33, 319 (2015).

  4. Piccolo, S.R. & Frampton, M.B. Gigascience 5, 30 (2016).

    Article  Google Scholar 

  5. Masca, N.G.D. et al. eLife http://dx.doi.org/10.7554/eLife.05519 (2015).

  6. LeVeque, R.J., Mitchell, I.M. & Stodden, V. Comput. Sci. Eng. 14, 13–17 (2012).

    Article  Google Scholar 

  7. Garijo, D. et al. PLoS One 8, e80278 (2013).

    Article  Google Scholar 

  8. Loman, N. & Watson, M. Nat. Biotechnol. 31, 996–998 (2013).

    Article  CAS  Google Scholar 

  9. Bray, N.L., Pimentel, H., Melsted, P. & Pachter, L. Nat. Biotechnol. 34, 525–527 (2016).

    Article  CAS  Google Scholar 

  10. Steinbiss, S. et al. Nucleic Acids Res. 44 1, W29–34 (2016).

    Article  CAS  Google Scholar 

  11. Sadedin, S.P., Pope, B. & Oshlack, A. Bioinformatics 28, 1525–1526 (2012).

    Article  CAS  Google Scholar 

  12. Belmann, P. et al. Gigascience 4, 47 (2015).

    Article  Google Scholar 

  13. Moreews, F. et al. F1000Res 4, 1443 (2015).

    Article  Google Scholar 

  14. Hosny, A., Vera-Licona, P., Laubenbacher, R. & Favre, T. Bioinformatics 32, 2396–2398 (2016).

    Article  CAS  Google Scholar 

  15. Perkel, J. Nature 538, 127–128 (2016).

    Article  CAS  Google Scholar 

  16. Köster, J. & Rahmann, S. Bioinformatics 28, 2520–2522 (2012).

    Article  Google Scholar 

  17. Di Tommaso, P. et al. PeerJ 3, e1273 (2015).

    Article  Google Scholar 

  18. Goecks, J., Nekrutenko, A. & Taylor, J. Genome Biol. 11, R86 (2010).

    Article  Google Scholar 

  19. Blankenberg, D. et al. Genome Biol. 15, 403 (2014).

    Article  Google Scholar 

  20. Vivian, J. et al. Preprint at bioRxiv http://biorxiv.org/content/early/2016/07/07/062497 (2016).

    Google Scholar 

  21. Stamatakis, A. Bioinformatics 22, 2688–2690 (2006).

    Article  CAS  Google Scholar 

  22. Byron, S.A., Van Keuren-Jensen, K.R., Engelthaler, D.M., Carpten, J.D. & Craig, D.W. Nat. Rev. Genet. 17, 257–271 (2016).

    Article  CAS  Google Scholar 

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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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  5. Emilio Palumbo
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  6. Cedric Notredame
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Corresponding author

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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