Containers and Workflow Pipelines for reproducible and automated data analysis
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.
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)
Bioinformaticians with no or little knowledge of containers or workflow pipelines.
You're familiar with doing bioinformatics on the command-line.
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
Ghent - Clemenspoort
Overwale 3
9000 Ghent
Belgium
11 May 2020 - 12 May 2020
Ghent - Clemenspoort
The Clemenspoort, the Clemenshuis, and the Clemenshof are integrated into a network of other buildings on the grounds of the former Redemptorist monastery, now the Overwale street.
Located just 250 meters from Ghent St. Pieters Station.
11 May 2020 - 12 May 2020
Ghent - Clemenspoort
40 bike parking lots available.
11 May 2020 - 12 May 2020
Ghent - Clemenspoort
Parking facilities available (€ 1.80 per hour). GPS address: Sint-Denijslaan 251. Take the driveway of the HoGent Sports Hall (not the HoGent Campus) and drive all the way to the end - past the HoGent parking areas. If you are registered in the 411 app, activate your license plate under the option 'Garage parking via license plate'. The barrier will open automatically, and payment will be processed via 4411.
11 May 2020 - 12 May 2020
Ghent - Clemenspoort
+32 476 46 10 40