Nextflow Course 2023 Fall

Reproducible research and data analysis using Nextflow

About the course

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

Outline

The course will train participants to build Nextflow pipelines and run them with Linux containers.

It is designed to provide trainees with short and frequent hands-on sessions while keeping theoretical sessions to a minimum.

Learning objectives

• 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.
• Understand, run and build Linux containers
• Use containers in Nextflow processes
• 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 are online on the dedicated GitHub page for self-learning.

Practitioners will need to connect during the course to a remote server via the "ssh" protocol. 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 on the server) or to be able to use an editor able to connect remotely. For the sake of information, below are the basics of "nano": https://wiki.gentoo.org/wiki/Nano/Basics_Guide

Having a GitHub account is recommended.

Knowing concepts about Linux containers is recommended.

Dates, time, location

• Dates: From 12th of September to 15th of September 2023.

• Time: 12/09/23 9:30 - 17:00h (CET)

• Time: 13-14-15 09/23 9:30 - 13:00h (CET)

• Location: Training room, CRG.

Program

Day 1: Understand and run a basic Nexflow pipeline

• 09:30-11:00 Introduction to Nextflow
• 11:00-11:30 Coffee break
• 11:30-13:00 Making simple scripts: channels operators and workflows

Day 1: Write, modify, and run a complex pipeline

• 14:30-15:30 More complex scripts:
• 15:30-16:00 Coffee break
• 16:00-17:00 Directive and resuming

Day 2: Linux containers

• 09:30-11:00 - Linux containers: Docker & Singularity/Apptainer
• 11:00-11.30 - Coffee break
• 11:30-13.00 - Decoupling resources, parameters and main script

Day 3: Run a Nextflow pipeline in different environments

• 09:30-11:00 Singularity and more processes
• 11:00-11:30 Coffee break
• 11:30-13:00 Profiles and cloud

Day 4: Nextflow modules and Tower

• 09:30-11:00 Modules
• 11:00-11:30 Coffee break
• 11:30-13:00 Tower

Acknowledgements

• Sphinx. The publication system for our course pages.