About the course
This slow-paced hands-on internal course is designed for absolute beginners who want to start using Nextflow DSL2 to achieve reproducibility of the data analysis.
Luca Cozzuto |
Toni Hermoso |
Julia Ponomarenko |
---|---|---|
Outline
This Linux Containers and Nextflow course will train participants to build Nextflow pipelines and run them with Singularity containers.
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. The link will be provided via the CRG learning platform.
Learning objectives
Locate and fetch Nextflow pipelines from dedicated repositories.
Execute/Run a Nextflow pipeline.
Describe and explain Nextflow basic concepts.
Test and modify a Nextflow pipeline.
Implement short blocks of code into a Nextflow pipeline.
Develop a Nextflow pipeline from scratch.
Run a pipeline in diverse computational environments (local, HPC, cloud).
Share a pipeline.
Prerequisite / technical requirements
Being comfortable working with the CLI (command-line interface) in a Linux-based environment. Knowledge of containers is not mandatory. The course materials is online in the dedicated GitHub page for self-learning.
Practitioners will need to connect during the course to a remote server via the “ssh” protocotol. You can learn about it here
Those who follow the course should be able to use a command-line/screen-oriented text editor (such as nano or vi/vim, which are already available in the server) or to be able to use an editor able to connect remotely. For sake of information, below the basics of nano
Having a GitHub account is recommended.
Dates, time, location
Dates: Jun 30 - July 1, 2022.
9:30 - 17:00 CET
Location: CRG training room.
Suggested program
Day 1: Understand and run a basic Nexflow pipeline (June 30)
09:30-11:00 Introduction to Nextflow
11:00-11:30 Coffee break
11:30-13:30 Making simple scripts: channels operators and workflows
Day 1: Write, modify and run a complex pipeline (Jun 30)
14:30-15:30 More complex scripts: Directive and resuming
15:30-16:00 Coffee break
16:00-17:00 Decoupling resources, parameters and main script
Day 2: Run a Nextflow pipeline in different environments (Jul 1)
09:30-11:00 Singularity and more processes.
11:00-11:30 Coffee break
11:30-13:30 Profiles and cloud
Day 2: Nextflow modules and Tower
14:30-15:30 Modules
15:30-16:00 Coffee break
16:00-17:00 Tower