Courses@CRG: Reproducible research and data analysis using Containers & Nextflow 2022

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, instructors and speakers:

	Luca Cozzuto CRG Bioinformatics Unit		José Espinosa Notredame's Lab
	Toni Hermoso CRG Bioinformatics Unit		Phill Ewels Sequera Lab
	Julia Ponomarenko CRG Bioinformatics Unit		Cedric Notredame Notredame's Lab
	Leila Mansouri Notredame's Lab		Suzanne Jin Notredame's Lab
	Athanasios Baltzis Notredame's Lab		Alessio Vignoli Notredame's Lab
	Luisa Santus Notredame's Lab		Emilio Palumbo Guigó's Lab

Dates:

• Dates: 30th May until 3rd June 2022 and additionaly 7th of June 2022
• Time: 9:30 - 13:30h (CET)
• Location: Online - Via Zoom 

Outline:

The 6-half 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.

The course will be fully virtual via the Zoom platform.

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 )

More information about the programme TBA soon.

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: 30

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

Registration:

Registration is free

Deadline: 15th May 2022

Registration: HERE

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

Contact:

Centre for Genomic Regulation

Barcelona Biomedical Research Park (PRBB)

Dr. Aiguader 88

08003 Barcelona

Spain