Linux Containers and Nextflow for reproducible research and open science
Linux Containers and Nextflow for reproducible research and open science
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 a 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:
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Julia Ponomarenko |
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Antonio Hermoso |
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Luca Cozzuto |
Learning objectives:
About containers:
- 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.
About Nextflow:
- 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 )
Dates:
- 7th - 11th February 2022 - 9:30 - 16:30
- Location: Online - Via Zoom
Number of participants:
Approximately 20 (as the course is online the number is flexible)
Prerequisites:
Being comfortable working with the CLI (command-line interface) in a Linux-based environment. Applicants are not expected to have worked with Nextflow workflows before.
Contact:
Dr. Aiguader 88
08003 Barcelona
The PHINDaccess project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 811.034.
