Bioinformatics Team Leader, SciLifeLab, Sweden
nf-core (http://nf-co.re) is a community effort to collect, curate and collaborate on high quality nextflow bioinformatics workflows. Shared pipelines give increased reproducibility between groups and greater collective development power. To help users and developers we have written an nf-core companion tool with a workflow template, code linting and helper functions for downloading pipelines for offline use and staying up to date. All nf-core 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.
Now in its second year, the nf-core community continues to develop at a rapid pace. More and more pipelines are being added to the list of stable releases, and the suite of framework tools continues to grow. In this talk I will describe recent updates from the nextflow nf-core community - what’s new with pipelines, best-practices, tips & tricks and the nf-core companion tools.
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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