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Nextflow for beginners - 3-day course (19.04; 26.04; 3.05), Tartu - Course is full

This 3-day Nextflow course by ELIXIR Estonia, in collaboration with the University of Tartu HPC Center, comprehensively introduces the powerful workflow language. Nextflow is renowned for its robust, scalable, and reproducible methods of running computational pipelines. Through efficient, interactive lessons, participants will gain a solid understanding of Nextflow technology, from fundamental to advanced concepts.

General info

  • Time:
    • Day 1: 19.04.2024 9:00-17:00
    • Day 2: 26.04.2024 9:00-17:00
    • Day 3: 3.05.2024 9:00-17:00
  • Type: Workshop
  • Language: English
  • Duration: all day - 8 h
  • Location: Delta building, Narva mnt 18, Tartu
    • Day 1: Room 2006
    • Day 2: Room 2030
    • Day 3: Room 2006
  • Audience: students, researchers. Beginner level
  • Lecturer: Nurlan Kerimov, PhD
  • Assistants: Ivan Kuzmin, Ralf Tambets, Peep Kolberg


The course ensures that participants receive frequent hands-on experience while minimising theoretical sessions. By the end of this course, participants are expected to possess the necessary proficiency to develop, use and deploy their own workflows using Nextflow. Additionally, participants will receive an introduction to nf-core pipelines, gaining insights into how these ready-to-use pipelines can be integrated into their workflows for enhanced bioinformatics analysis. This component of the course aims to provide a comprehensive understanding of both Nextflow and nf-core, ensuring participants can effectively utilize these tools in their projects. All essential course materials and software installation guidelines will be available on a GitHub repository. This course will equip participants with the skills to effectively build and execute Nextflow pipelines.


  • Applicants should be comfortable working with the CLI (command-line interface) in a Linux-based environment. If you feel uncomfortable with UNIX commands, refresh your knowledge with the UNIX Shell course materials here.
  • Participants must be able to connect during the course to a remote server via the “SSH” protocol. You can learn how ssh works here.
  • Instructor will be using VS Code with SSH extension; it is recommended to use the same text editor for ease of comparison.
  • Participants need to bring their laptop. 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 to learn how to run pipelines in different computation environments.


  • Day 1:
    • Introduction to Nextflow.
    • Learning the building blocks 1
  • Day 2:
    • Learning the building blocks 2
    • Understand, develop and run a basic Nextflow pipeline
  • Day 3:
    • Use HPC to run the pipeline
    • Introduction to nf-core and running nf-core pipelines

Learning outcomes for the participants:

  • 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.
  • Locate and fetch Nextflow pipelines from dedicated repositories.
  • Run a pipeline in diverse computational environments (local, HPC, cloud).
  • Get acquainted with nf-core pipelines and their usage.
  • Share a pipeline.


We ask you to register responsibly. If you can’t attend the lecture, please let us know as soon as possible via email (

Register: Course is full

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