Containers & Workflow pipelines workshop#

Welcome to our Nextflow workshop! We are very happy to have you here.

General context#

This is the third edition of this workshop, jointly organised by the VIB Bioinformatics Core and ELIXIR Belgium.

  • The first session (15 & 16 April 2024) is dedicated to Containers (Docker & Singularity) which are great tools for code portability and reproducibility of your analysis. You will learn how to use containers and how to build a container from scratch, share it with others and how to re-use and modify existing containers.

  • The second session (23 & 24 May 2024) is focused on Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. Starting from the basic concepts we will build our own simple pipeline and add new features with every step. On the second day, we will utilise all the gathered knowledge to build a small-scale microbiomics pipeline.

This website contains the course materials and outline for the second session.

The presentation which goes alongside this material can be found here. The presentation shared by nf-core in thier participation can be found here

Practical information#

Schedule day 1:

  • 9:30 - 11:00 - session

  • 11:00 - 11:15 - break

  • 11:15 - 12:45 - session

  • 12:45 - 13:45 - lunch

  • 13:45 - 15:15 - session

  • 15:15 - 15:30 - break

  • 15:30 - 17:00 - session

We aim to complete up to and including exercise 2.5 during this day

Schedule day 2:

  • 9:30 - 11:00 - session

  • 11:00 - 11:15 - break

  • 11:15 - 12:45 - session

  • 12:45 - 13:45 - lunch

  • 13:45 - 14:45 - nf-core presentation

  • 14:45 - 17:00 - project

Objectives#

The objectives of the Nextflow workshop are the following:

  • Understand Nextflow’s basic concepts & syntax: channels, processes, modules, workflows, etc.

  • Execute local and publicly available pipelines with different executors and environments

  • Write and run Nextflow pipelines

  • Write and modify config files for storing parameters related to computing hardware as well as pipeline dependent parameters

Prerequisites#

Being comfortable working with the CLI (command-line interface) in a Linux-based environment.

Requirements#

The (technical) installation requirements are described in the installations section.

Exercises#

The exercises and solutions are available in this GitHub repository.