DESCRIPTION
Nextflow is a workflow system designed to simplify the creation of bioinformatics pipelines. This system allows bioinformaticians to write pipelines that are scalable, reproducible, and portable, which is particularly critical in the public health laboratories. Nfcore project is complementary to Nextflow and is a community driven effort to develop a standardized framework for writing Nextflow pipelines, as well as a curated database of those pipelines.
This training will provide participants the opportunity to learn Nextflow and the nf-core framework for pipeline development. This three-day, in-person event will include participatory live coding and hands-on exercises. Instructors will teach lesson material by typing code, and training participants will code alongside instructors. Each lesson will include practical exercises that allows participants to test their knowledge as they learn. By the end of the training, participants should have the skills necessary to code a simple pipeline in Nextflow using the nf-core framework.
AUDIENCE
This course is appropriate for bioinformaticians or data scientists in state, territorial or local public health laboratories. Participants should be familiar with the utilization of command line environments for R/python scripting and tool development. Ideal participants will have the ability to write their own bioinformatic pipelines, and should have a working knowledge of Git/GitHub, as well as familiarity with containerization processes (Docker/Singularity/Conda).
OBJECTIVES
At the conclusion of the program, the participant will be able to:
- Identify the fundamental components of a Nextflow workflow
- Describe the core features and key benefits of the nf-core project
- Recognize and subsequently utilize a community curated nfcore pipeline
- Write a multi-step workflow to process and analyze next generation sequencing data with Nextflow using the nf-core framework
FACULTY
Kelsey Florek, PhD, MPH, senior genomics and data scientist, Wisconsin State Laboratory of Hygiene
Christopher Jossart, MPH, data scientist II, Wisconsin State Laboratory of Hygiene
Abigail Shockey, PhD, bioinformatician, Wisconsin State Laboratory of Hygiene
Erin Young, PhD, bioinformatician, Utah Public Health Laboratory
ACCESSIBILITY
In compliance with the Americans with Disabilities Act, individuals seeking special accommodations must email a request to Shannon Mahoney (Shannon.mahoney@aphl.org) at least three weeks prior to the workshop’s start date
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