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 |
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Dates, time, location
Dates: From 6th of February to 9th of February 2024.
Location: ALBA.
Program
Day 1: Understand and run a basic Nexflow pipeline
10:00-11:00 Introduction to Nextflow
11:00-11:30 Break
11:30-13:00 Making simple scripts: channels operators and workflows
Day 1: Write, modify, and run a complex pipeline
14:30-15:30 More complex scripts
15:30-16:00 Break
16:00-17:30 Directive and resuming
Day 2: Linux containers
14:00-15:00 - Linux containers. Docker introduction and running
15:00-15.30 - Break
15:30-17.00 - Building Docker containers. Singularity/Apptainer
Day 3: Run a Nextflow pipeline in different environments
14:00-15:00 Singularity and more processes
15:00-15.30 Break
15:30-17.00 Profiles and cloud
Day 4: Nextflow modules and Tower
14:00-15:00 Modules
15:00-15.30 Break
15:30-17.00 Tower
Outline
This Nextflow course will train participants to build Nextflow pipelines and run them with Linux containers.
Learning objectives
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.
Understand, run and build Linux containers
Use containers in Nextflow processes
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.
Having a GitHub account is recommended.