Head of Genomics Applications Development at SciLifeLab National Genomics Infrastructure, Sweden
The Swedish National Genomics Infrastructure (NGI) has been a key user and proponent of nextflow since soon after its initial release. We have produced several popular pipelines as well as writing recommendations on best practices. Our oldest pipeline for RNA sequencing analysis is used in production at NGI Stockholm and has been used to process nearly 20,000 samples since April 2017.
The open-source NGI pipelines hosted on GitHub have now been forked by hundreds of users for their own development. This collaborative expansion has proceeded rapidly and is now beginning to outgrow the NGI branding of the pipelines. To encourage further growth and greater collaboration, we started a new initiative called nf-core: a community effort to collect, curate and collaborate on high quality nextflow bioinformatics workflows.
Shared pipelines will give increased reproducibility between groups and greater collective development power. To help pipeline developers we have written a companion cookiecutter template to generate starter workflows and a command line tool to lint code and check for adherence to nf-core guidelines. Pipelines make the best use of Nextflow features possible, with support for Conda, Docker and Singularity, with reference genomes available from the cloud. Consistency between pipelines means that all work in a similar manner with comparable requirements.
There has been fantastic feedback from the user community about nf-core. The first twitter post in February 2018 was seen by nearly four thousand people and the account now has over 140 followers. There are currently seven pipelines available (at the time of writing) with many more on the way.
Phil Ewels is the head of the Genomics Applications Development facility at the National Genomics Infrastructure (NGI) at SciLifeLab in Stockholm, Sweden. SciLifeLab is a national centre for molecular biosciences for Sweden; the NGI is the largest platform at SciLifeLab. We provide library preparation, sequencing and bioinformatics analysis support for research groups across the country.
Phil has been working at SciLifeLab for four years and moved to Sweden after a PhD and postdoc at the University of Cambridge and Babraham Institute in Cambridge, UK. He has has a history of lab and bioinformatics work in epigenetics and has a soft spot for software development with a focus on user friendliness. More recently he’s developed MultiQC - a tool that parses log file outputs from multiple samples and bioinformatics tools and generates a single interactive HTML report. Now head of the Genomics Applications Development facility, he and his team focus on the development and scaling up of new lab protocols and bioinformatics solutions for the ISO accredited NGI Genomics Production facility. They develop new analysis pipelines and try to ensure that the tools they write are scalable, reproducible and transferable.
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