ELIXIR Nextflow course 22.-23.11.2021 Tartu

Overview

Nextflow is a powerful polyglot workflow language that provides a robust, scalable and reproducible way to run computational pipelines. In very practical and interactive sessions, participants will learn about Nextflow technology starting from basic through more advanced concepts, with the expectation they will acquire the proficiency to develop and deploy their own workflows.

This 2-day course will train participants to build Nextflow pipelines and run them. It is designed to provide participants with short and frequent hands-on sessions, while keeping theoretical sessions to a minimum.

A GitHub repository will be provided with all the necessary material and software installation guidelines.

Audience

This hands-on course is designed for absolute beginners who want to start using Nextflow to achieve reproducibility of data analysis. 

Learning outcomes

At the end of the course, participants are expected to be able to:

  • Develop a Nextflow pipeline from scratch.
  • Describe and explain Nextflow's basic concepts.
  • Implement short blocks of code into a Nextflow pipeline.
  • Execute/Run a Nextflow pipeline.
  • Test and modify a Nextflow pipeline.
  • Locate and fetch Nextflow pipelines from dedicated repositories.
  • Run a pipeline in diverse computational environments (local, HPC, cloud).
  • Share a pipeline.

Prerequisites

Knowledge / competencies

Applicants should be comfortable working with the CLI (command-line interface) in a Linux-based environment. If you do not feel comfortable with UNIX commands, you can refresh your knowledge with the UNIX Shell course materials here.

Participants will need to connect during the course to a remote server via the "ssh" protocol. You can learn how does ssh work in here.

Participants 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. Instructor will be using VS Code with SSH extension, it is recommended to use the same text editor for ease of comparison. 

Knowledge of containers is not mandatory; however, recommended. 

Participants are preferred to bring their own laptop but also local Linux computers can be used (please let us know about it during the registration). They will work in their local machine to learn the basics and develop their very first pipeline. They will also work in a dedicated UT HPC environment in order to learn running pipelines in different computation environments. 

Schedule

22.11.2021 Day 1: Introduction to Nextflow. Learning the building blocks

23.11.2021 Day 2: Understand, develop and run a basic Nextflow pipeline

The course runs from 10.15-18.00.

Registration

Please register responsively. Due to COVID-19 situation we accept only fully vaccinated persons who must bring and show the vaccination certificate AND take a rapid antigen test before the course starts during Day 1 (9.30 on Monday 22.11.2021). We accept up to 12 people for the course based on the data submitted to the registration form.

This course description is adapted from SIB Nextflow course page.