Containers and Workflow Pipelines for reproducible and automated data analysis

Containers and Workflow Pipelines for reproducible and automated data analysis

Target Audience:
11 May 2020
12 May 2020

General context

POSTPONED! This course will be postponed to a later date. The participants will be noticed of further changes.

This two day course is organized jointly by the Bioinformatics core facility of the Centre for Genomic Regulation, Barcelona, Spain and ELIXIR Belgium.  

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

On the second day, you will learn how to use Nextflow for building scalable and reproducible bioinformatics pipelines and running them on a personal computer, cluster and cloud. 

 

Objectives

Containers

  • Learn the concept of and the difference between Docker & Singularity containers 
  • Write a Docker recipe, build and run a Docker image and containers
  • Pull and push Docker container to / from Docker hub
  • Docker files and layers; Docker cashing
  • Working with volumes
  • Pull Docker containers as a Singularity image

Pipelines

  • Understand Nextflow's basic concepts: processes, channels, ...
  • Write and run a Nextflow pipeline (using a Singularity containers)
Event intended for

Bioinformaticians with no or little knowledge of containers or workflow pipelines. 

Required skills

You're familiar with doing bioinformatics on the command-line. 

Trainers

Toni Hermoso Pulido
Centre for Genomic Regulation, Barcelona

Toni Hermoso Pulido is an expert in bioinformatics software, databases and web services. He holds the degree in Biochemistry and the PhD in Biotechnology from the Autonomous University of Barcelona, Spain.

Luca Cozzuto
Centre for Genomic Regulation, Barcelona

Luca Cozzuto is an expert in high-throughput sequencing data analysis and bioinformatics pipeline development. He holds the SciD in Pharmaceutical Biotechnologies and a PhD in molecular medicine from the University of Naples Federico II, Italy.

Sarah Bonnin
Centre for Genomic Regulation, Barcelona

Sarah Bonnin is an an expert in high-throughput sequencing data analysis and bioinformatics training. She obtained the BSc in Biology at the University Claude Bernard Lyon 1, France and the MSc in Bioinformatics at the University Denis Diderot Paris 7, France.

Program

Docker Containers
-
Introduction to containers
-
  • History of containers, what are containers and why should we use them? 
  • Containers vs. virtual machines
Singularity Containers
-
  • Differences between Singularity and Docker: why and when to use one or the other. Pros and cons.
  • Singularity recipes
  • Building a basic Singularity image
  • Pull and run an image with Singularity from Docker hub
  • Volumes in Singularity
  • Use a Singularity image interactively
Nextflow pipelines
-
  • Run a simple Nextflow pipeline & obtain a thorough understanding of config and pipeline files
  • Modifying a pipeline and rerun processes
  • Theoretic approach to processes, channels and operators; the basics of Nextflow
  • Write and run a simple Nextflow pipeline (e.g. print text, process a simple calculation)
  • Including Singularity containers in Nextflow pipelines

Practical info

11 May 2020 - 12 May 2020

Clemenspoort Gent

Overwale 3
9000 Ghent
Belgium

11 May 2020 - 12 May 2020

Clemenspoort Gent
Public transport

The train station Ghent St-Pieters is only 250 m away. We have 40 bike lots.

11 May 2020 - 12 May 2020

Clemenspoort Gent
Parking

We offer parking lots (1.20 € per hour). GPS address: Sint-Denijslaan 251.
Please take the neem the exit SPORTHAL HoGent (not Campus HoGent) and drive all the way to the end, so past the parking slots of HoGent.

11 May 2020 - 12 May 2020

Clemenspoort Gent
Location contact

+32 476 46 10 40

info@clemenspoort.be

Contact

VIB training
Tel: +32 9 244 66 11
Mail: training@vib.be