Courses@CRG: Reproducible research and data analysis using Containers & Nextflow 2022
About the course:
This slow-paced hands-on course is designed for absolute beginners who want to start using containers and Nextflow pipelines to achieve reproducibility of data analysis. Linux containers allow the storage of code and applications in an host-independent lightweight environment. They became a fast and popular way to share and deploy applications in different environments. Nextflow is a powerful polyglot workflow language that, coupled with Docker and Singularity containers, provides a robust, scalable and reproducible way to run computational pipelines.
Organizers, instructors and speakers:
- Luca Cozzuto, CRG Bioinformatics Unit
- José Espinosa, Notredame's Lab
- Toni Hermoso, CRG Bioinformatics Unit
- Phill Ewels, Sequera Lab
- Julia Ponomarenko, CRG Bioinformatics Unit
- Cedric Notredame, Notredame's Lab
- Leila Mansouri, Notredame's Lab
- Susanne Jin, Notredame's Lab
- Athanasios Baltzis, Notredame's Lab
- Alessio Vignoli, Notredame's Lab
- Luisa Santus, Notredame's Lab
- Emilio Palumbo, Guigó's Lab
- Dates: 30th May until 3rd June 2022 and additionaly 7th of June 2022
- Time: 9:30 - 13:30h (CET)
- Location: Online - Via Zoom
The 6-half day course will train participants to use and build Docker and Singularity containers and Nextflow pipelines.
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.
Trainees will work in a dedicated AWS Cloud9 environment.
- Locate and fetch Docker/Singularity images from dedicated repositories.
- Execute/Run a Docker/Singularity container from the command line.
- Build Docker container from an existing recipe.
- Design/Write a Docker recipe.
- Convert Docker to Singularity image.
- Locate and fetch Nextflow pipelines from dedicated repositories.
- Execute/Run a Nextflow pipeline.
- Describe and explain Nextflow's basic concepts.
- Test and modify a Nextflow pipeline.
- Implement short blocks of code into a Nextflow pipeline.
- Develop a Nextflow pipeline from scratch.
- Run pipeline in diverse computational environments (local, HPC, cloud )
More information about the programme TBA soon.
Being comfortable working with the CLI (command-line interface) in a Linux-based environment. Applicants are not expected to have used neither Linux containers nor Nextflow workflows before.
Number of participants: 30
Registration is free
Deadline EXTENDED: 15th May 2022!
Shortly after the application deadline, participants will be informed if they have been accepted for the course.