About the course
This slow-paced hands-on 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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Other instructors:
Alessio Vignoli
Athanasios Baltzis
Jose Espinosa-Carrasco
Leila Mansouri
Bjorn Langer
Suzanne Jin
Emilio Palumbo
Edgar Garriga Nogales
Outline
The 4-half-day 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.
Trainees will work in a dedicated AWS environment.
Learning objectives
Locate and fetch Docker/Singularity images from dedicated repositories.
Execute/Run a Docker/Singularity container from the command line.
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; however, this SIB course can be advised to take. 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: November 15-18, 2021
- Time: 13:00-17:30 CET
Afternoon coffee break: 15:00-15:30
Location: virtual, via Zoom.
Program
Day 1: Introduction to Nextflow and Linux containers
13:00-13:30 Getting started, become familiar with the working environment.
13:30-14:30 Talk by Cédric Notredame and Jose Antonio Espinosa, Comparative Bioinformatics, CRG.
14:30-15:00 Introduction to Docker and Singularity containers.
15:00-15:30 Break.
15:30-16:30 Docker hub, BioContainers and other repositories. Find existing containers. Execute a Singularity container.
16:30-17:30 Nexflow: introduction, installation, run a simple pipeline.
Day 2: Understand and run a basic Nexflow pipeline
13:00-14:00 Nexflow basic concepts. Channels and Operators. Processes, Workflows and the log.
14:00-14:30 Breakout rooms: create channels starting from data. Write and run a simple pipeline.
14:30-15:00 Troubleshooting, Q&A.
15:00-15:30 Break.
15:30-16:30 Combining processes, directives, resuming a pipeline.
16:30-17:00 Breakout rooms: write and run a more complex pipeline.
17:00-17:30 Troubleshooting, Q&A.
Day 3: Write, modify and run a complex pipeline
13:00-14:00 Decoupling resources, parameters and nextflow script (params and nextflow config). Help section. How to get pipelines and run them.
14:00-14:30 Breakout rooms: example of directives, get a pipeline and run it with a test dataset.
14:30-15:00 Troubleshooting, Q&A.
15:00-15:30 Break.
15:30-16:30 Fetch public pipelines, adapt and run them.
16:30-17:00 Breakout rooms: exercise.
17:00-17:30 Troubleshooting, Q&A.