This hands-on course is designed for bioinformatitians 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.
Number of course hours : 18 hours
Date : 12th -15th September 2023
Level: Beginners
Topics Covered:
- 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).