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nf-core: Community curated bioinformatics pipelines

View ORCID ProfilePhilip A Ewels, View ORCID ProfileAlexander Peltzer, View ORCID ProfileSven Fillinger, View ORCID ProfileJohannes Alneberg, View ORCID ProfileHarshil Patel, View ORCID ProfileAndreas Wilm, View ORCID ProfileMaxime Ulysse Garcia, View ORCID ProfilePaolo Di Tommaso, View ORCID ProfileSven Nahnsen
doi: https://doi.org/10.1101/610741
Philip A Ewels
1Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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  • ORCID record for Philip A Ewels
Alexander Peltzer
2Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
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Sven Fillinger
2Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
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Johannes Alneberg
1Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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Harshil Patel
3Bioinformatics and Biostatistics, The Francis Crick Institute, London, United Kingdom
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Andreas Wilm
4Computational & Systems Biology, Genome Institute of Singapore, Singapore
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Maxime Ulysse Garcia
5Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
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Paolo Di Tommaso
6Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
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Sven Nahnsen
2Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
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  • For correspondence: sven.nahnsen@qbic.uni-tuebingen.de
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Abstract

The standardization, portability, and reproducibility of analysis pipelines is a renowned problem within the bioinformatics community. Most pipelines are designed for execution on-premise, and the associated software dependencies are tightly coupled with the local compute environment. This leads to poor pipeline portability and reproducibility of the ensuing results - both of which are fundamental requirements for the validation of scientific findings. Here, we introduce nf-core: a framework that provides a community-driven, peer-reviewed platform for the development of best practice analysis pipelines written in Nextflow. Key obstacles in pipeline development such as portability, reproducibility, scalability and unified parallelism are inherently addressed by all nf-core pipelines. We are also continually developing a suite of tools that assist in the creation and development of both new and existing pipelines. Our primary goal is to provide a platform for high-quality, reproducible bioinformatics pipelines that can be utilized across various institutions and research facilities.

Footnotes

  • Various points addressed, clearer language and lots of minor edits to make the entire manuscript easier to read for a wider audience.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 24, 2019.
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nf-core: Community curated bioinformatics pipelines
Philip A Ewels, Alexander Peltzer, Sven Fillinger, Johannes Alneberg, Harshil Patel, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso, Sven Nahnsen
bioRxiv 610741; doi: https://doi.org/10.1101/610741
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nf-core: Community curated bioinformatics pipelines
Philip A Ewels, Alexander Peltzer, Sven Fillinger, Johannes Alneberg, Harshil Patel, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso, Sven Nahnsen
bioRxiv 610741; doi: https://doi.org/10.1101/610741

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