Workshops and courses

ELIXIR node event Nextflow for beginners - 3-day course

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Date: 19 April 2024 @ 09:00 - 17:00

Timezone: Tallinn

Duration: 8h + 8h + 8h

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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.

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.

Keywords: Command line, Data management, Bioinformatics, HPC, Nextflow

Venue: Narva mnt 18, 18 Narva maantee

City: Tartu

Country: Estonia

Postcode: 51009

Prerequisites:

  • 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.

Learning objectives:

  • 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.

Organizer: ELIXIR Estonia

Host institutions: University of Tartu, Institute of Computer Science

Eligibility:

  • First come first served

Target audience: Beginner

Capacity: 20

Event types:

  • Workshops and courses

Cost basis: Free to all

Scientific topics: Informatics

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