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Highlighted in 'Reproducibility, Standards and SOP in Bioinformatics' Workshop Collection

Using the Nextflow framework for reproducible in-silico omics analyses across clusters and clouds

, , ,
1 Center for Genomic Regulation (CRG), Barcelona, Spain
2 Universitat Pompeu Fabra (UPF), Barcelona, Spain
DOI
10.7287/peerj.preprints.2796v1
Published
Accepted
Subject Areas
Bioinformatics
Keywords
bionfomatics, pipeline, workflow, docker, container, reproducibility
Copyright
© 2017 Di Tommaso et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Di Tommaso P, Floden E, Chatzou M, Notredame C. 2017. Using the Nextflow framework for reproducible in-silico omics analyses across clusters and clouds. PeerJ Preprints 5:e2796v1

Abstract

Reproducibility has become one of biology’s most pressing issues. This impasse has been fuelled by the combined reliance on increasingly complex data analysis methods and the exponential growth of biological datasets. Nextflow is a pipeline orchestration tool that has been designed to ease deployment and guarantee reproducibility across platforms. It allows the seamless parallelization and deployment of any existing application with minimal development and maintenance overhead, irrespective of the original programming language. These capabilities guarantee consistent results over time and across different computing platforms.

Author Comment

This poster was submitted to CHARME / EMBnet / NETTAB 2016 Workshop.

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Paolo Di Tommaso conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Evan Floden conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Maria Chatzou conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.

Cedric Notredame conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

The research in this article did not generate, collect or analyse any raw data or code.

Funding

The authors received no funding for this work.

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Using the Nextflow framework for reproducible in-silico omics analyses across clusters and clouds
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