Getting started with nf-core

Philip Ewels

Bioinformatics Team Leader, SciLifeLab, Sweden

The nf-core community provides a range of tools to help new users get to grips with nextflow - both by providing complete pipelines that can be used out of the box, and also by helping developers with best practices. Companion tools can create a bare-bones pipeline from a template scattered with TO-DO pointers and CI with linting tools check code quality. Guidelines and documentation help to get nextflow newbies on their feet in no time. Best of all, the nf-core community is always on hand to help.

In this tutorial we discuss the best-practice guidelines developed by the nf-core community, why they’re important and give insight into the best tips and tricks for budding nextflow pipeline developers.


Phil Ewels is the Team Leader for Bioinformatics development 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 five 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 at SciLifeLab, 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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