COURSE DESCRIPTION (OVERVIEW & PURPOSE)
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.
- 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 )
TYPE OF TRAINING
Post and under graduate students, postdocs, engineers working with computational pipelines
PLACE OF THE TRAINING
Streamed via Zoom from Center for Genomic Regulation, Barcelona, Spain.
Centre for Genomic Regulation, Barcelona, Spain
TRAINERS & AFFILIATIONS
Julia Ponomarenko (Genomic Regulation, Barcelona, Spain)
Luca Cozzuto (Genomic Regulation, Barcelona, Spain)
Toni Hermoso (Genomic Regulation, Barcelona, Spain)
Kais Ghedra (Institute Pasteur, Tunis)
NUMBER OF PARTICIPANTS
Approximately 20 (as the course is online the number is flexible)
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.