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Registration closed July 15.

BCC2020 is online, global, and affordable. The meeting and training are now done, and the CoFest is under way.

The 2020 Bioinformatics Community Conference brings together the Bioinformatics Open Source Conference (BOSC) and the Galaxy Community Conference into a single event featuring training, a meeting, and a CollaborationFest. Events run from July 17 through July 25, and is held in both the eastern and western hemispheres.

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Tuesday, July 21 • 22:15 - 22:20
What’s new with nf-core: community-built bioinformatics pipelines 🍐

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The presenter(s) will be available for live Q&A in this session (both hemispheres).

Philip Ewels 1, Alexander Peltzer 2,3, Harshil Patel 4, Gisela Gabernet 3, Maxime Ulysse Garcia 5, Olga Botvinnik 6, Sven Fillinger 4, Johannes Alneberg 7, Sven Nahnsen 2 and the nf-core & Nextflow communities.

1 Science for Life Laboratory (SciLifeLab), DBB, Stockholm University, Stockholm, Sweden. Email: phil.ewels@scilifelab.se
2 Translational Medicine and Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & CO. KG, Germany
3 Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
4 Bioinformatics and Biostatistics, The Francis Crick Institute, London, United Kingdom
5 Department of Oncology, Karolinska Institute, Stockholm, Sweden
6 Data Sciences Platform, Chan Zuckerberg Biohub, San Francisco, California, USA
7 Science for Life Laboratory (SciLifeLab), KTH, School of Biotechnology, Division of Gene Technology, Sweden

Project Website: https://nf-co.re/
Source Code: https://github.com/nf-core/ 
License: MIT License

Main Text of Abstract

Analysis pipelines and computational workflows are increasingly becoming a core component in life-science research. Standardisation of software packaging (bioconda, docker, singularity) can now come together with workflow managers and languages (Nextflow, Snakemake, CWL, WDL) to facilitate analysis workflows that can be truly portable across virtually any computational infrastructure (server, HPC, cloud).

Over the past two years nf-core has grown to be a truly global collaborative effort to collect goldstandard workflows built using Nextflow. All pipelines adhere to strict guidelines and are built using a common template, with consistent usage patterns and best-in-class testing and support.

The year since Alex Peltzer’s presentation at BOSC 2019 has been one of rapid growth and development. In this talk I will describe some of the major developments, including:

• Nearly double the community size, with over 1000 twitter followers and 500 GitHub contributors at time of writing (see https://nf-co.re/stats for details)
• Growth to 43 pipelines (11 new since BOSC 2019, with 8 newly stable)
• Publication of a manuscript in Nature Biotechnology describing the community
• New user-friendly tools to launch pipelines, using JSON schema describing parameters

I’ll also point to future developments coming soon, such as migration to Nextflow DSL2 with modular code and improved code testing: both unit testing and full-scale data tests.

avatar for Phil Ewels

Phil Ewels

Bioinformatics Lead, Science for Life Laboratory
Bioinformatician doing research into next-generation sequencing applications. Lead for Bioinformatics development at the National Genomics Infrastructure in Sweden, part of SciLifeLab.Projects: MultiQC, nf-core, SRA-Explorer, QC Fail, Cluster Flow.

Tuesday July 21, 2020 22:15 - 22:20 EDT