About the course

This slow-paced hands-on internal course is designed for absolute beginners who want to start using Nextflow DSL2 to achieve reproducibility of the data analysis.

Main instructors:

Luca Cozzuto

Toni Hermoso

Julia Ponomarenko

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Outline

This Linux Containers and Nextflow course will train participants to build Nextflow pipelines and run them with Singularity containers.

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. The link will be provided via the CRG learning platform.

Learning objectives

  • Locate and fetch Nextflow pipelines from dedicated repositories.

  • Execute/Run a Nextflow pipeline.

  • Describe and explain Nextflow basic concepts.

  • Test and modify a Nextflow pipeline.

  • Implement short blocks of code into a Nextflow pipeline.

  • Develop a Nextflow pipeline from scratch.

  • Run a pipeline in diverse computational environments (local, HPC, cloud).

  • Share a pipeline.

Prerequisite / technical requirements

Being comfortable working with the CLI (command-line interface) in a Linux-based environment. Knowledge of containers is not mandatory. The course materials is online in the dedicated GitHub page for self-learning.

Practitioners will need to connect during the course to a remote server via the “ssh” protocotol. You can learn about it here

Those who follow the course should be able to use a command-line/screen-oriented text editor (such as nano or vi/vim, which are already available in the server) or to be able to use an editor able to connect remotely. For sake of information, below the basics of nano

Having a GitHub account is recommended.

Dates, time, location

  • Dates: Jun 30 - July 1, 2022.

  • 9:30 - 17:00 CET

  • Location: CRG training room.

Suggested program

Day 1: Understand and run a basic Nexflow pipeline (June 30)

  • 09:30-11:00 Introduction to Nextflow

  • 11:00-11:30 Coffee break

  • 11:30-13:30 Making simple scripts: channels operators and workflows

Day 1: Write, modify and run a complex pipeline (Jun 30)

  • 14:30-15:30 More complex scripts: Directive and resuming

  • 15:30-16:00 Coffee break

  • 16:00-17:00 Decoupling resources, parameters and main script

Day 2: Run a Nextflow pipeline in different environments (Jul 1)

  • 09:30-11:00 Singularity and more processes.

  • 11:00-11:30 Coffee break

  • 11:30-13:30 Profiles and cloud

Day 2: Nextflow modules and Tower

  • 14:30-15:30 Modules

  • 15:30-16:00 Coffee break

  • 16:00-17:00 Tower