Courses@CRG: Reproducible computational pipelines with Nextflow

About the course

This hands-on course is designed for software engineers who want to start using containers and Nextflow pipelines to achieve reproducibility for data analysis. Linux containers allow the storage of code and applications in a host-independent lightweight environment, they became a fast and popular way to share and deploy applications in different environments, including HPC clusters. Nextflow is a powerful polyglot workflow language that, coupled with Docker and Singularity containers, provides a robust, scalable and reproducible way to run computational pipelines.

Instructors: CRG Bioinformatics Core Technology
Dates: February 2024

• 6th (10:00am-17:30pm) and
• 7th, 8th and 9th (14:00-17:30)

Location: ALBA synchrotron
Outline: The 4-day course will train participants to use and build Docker and Singularity containers and Nextflow pipelines. It is designed to provide trainees with short and frequent hands-on sessions, while keeping theoretical sessions to a minimum.

Learning Objectives

About containers:

• Locate and fetch Docker/Singularity images from dedicated repositories.
• Execute/Run a Docker/Singularity container from the command line.
• Build Docker container from an existing recipe.
• Design/Write a Docker recipe.
• Convert Docker to Singularity image.

About Nextflow:

• Locate and fetch Nextflow pipelines from dedicated repositories.
• Execute/Run a Nextflow pipeline.
• Describe and explain Nextflow's basic concepts.
• Test and modify a Nextflow pipeline.
• Implement short blocks of code into a Nextflow pipeline.
• Develop a Nextflow pipeline from scratch.
• Run pipeline in diverse computational environments (local, HPC, cloud)

Prerequisites

Being comfortable working with the CLI (command-line interface) in a Linux-based environment. Applicants are not expected to have used neither Linux containers nor Nextflow workflows before.
Number of participants: 20 max
Registration - HERE
Shortly after the application deadline, participants will be informed if they have been accepted for the course.
Registration deadline: 20th January 2024

Contact

CRG Training and Academic Office
training@crg.eu
Centre for Genomic Regulation
Barcelona Biomedical Research Park (PRBB)
Dr. Aiguader 88
08003 Barcelona
Spain