Courses@CRG: Containers & Nextflow

About the course:

This slow-paced hands-on course is designed for absolute beginners 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:

	Julia Ponomarenko CRG Bioinformatics Unit		Sarah Bonnin CRG Bioinformatics Unit
	Luca Cozzuto CRG Bioinformatics Unit		Antonio Hermoso CRG Bioinformatics Unit

Instructors:

	José Espinosa Notredame's Lab		Emilio Palumbo Guigó's Lab
	Leila Mansouri Notredame's Lab		Edgar Garriga Notredame's Lab
	Athanasios Baltzis Notredame's Lab		Alessio Vignoli Notredame's Lab

Dates:

• 3rd, 4th, 10th & 11th May 2021 - 9:30 - 17:30
• Location: Online - Via Zoom 

Outline:

The 4-day Containers and Nextflow 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.

The course will be fully virtual via the Zoom platform.

Trainees will work in a dedicated AWS Cloud9 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 )

More information about the programme HERE

Prerequisite:

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: 25

3 slots are reserved for the members of each of the following consortium: PHINDaccess, EASI-Genomics, Ris3-cat VEIS, and PrecisionTox

Registration:

Registration is free and the deadline is: 25th April 2021

Registration HERE

Contact

Dr. Aiguader 88
08003 Barcelona