Courses@CRG: Nextflow 2023

About the course:

This hands-on course is designed for bioinformatitians who want to start using containers and Nextflow pipelines to achieve reproducibility of data analysis. Linux containers allow the storage of code and applications in an host-independent lightweight environment. They became a fast and popular way to share and deploy applications in different environments. 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.
 

Organizers:

• CRG Bioinformatics Core Technology
• CRG Training and Academic Office (TAO)

Dates:

• Dates: 12th -15 September 2023
• Time: 9:30 - 17:00h (CET)
• Location: CRG Training centre (PRBB patio) 

Outline:

The 4-day 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.
Trainees will work in a dedicated AWS environment.

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: 18

Registration HERE

Agenda HERE

Shortly after the application dealine, participants will be informed if they have been accepted for the course.

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