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Nextflow Runcourse

  • Course summary

    Nextflow Run is a hands-on introduction to running reproducible and scalable data analysis workflows.

    Working through a series of goal-oriented exercises, you will learn the essentials of launching and managing Nextflow pipelines, understand how channels and operators enable parallel processing of multiple inputs, and use containers to manage software dependencies.

    You will take away the skills and confidence to start running workflows with Nextflow.

  • Additional information

    Technical requirements

    You will need a GitHub account OR a local installation of Nextflow. Our training courses are compatible with Nextflow version 25.10.2 or later and require the use of the v2 parser EXCEPT the Hello nf-core course, which requires the v1 parser. See Environment options for more details.

    Learning objectives
    • Launch and manage Nextflow pipelines from the command line
    • Understand how channels and operators enable efficient multi-input, multi-step workflows
    • Use containers to manage software dependencies and ensure reproducibility
    • Configure pipeline execution and generate execution reports
    Audience & prerequisites
    • Audience: This course is designed for learners who are completely new to Nextflow and want to run existing pipelines.
    • Skills: Some familiarity with the command line, basic scripting concepts and common file formats is assumed.
    • Domain: The exercises are all domain-agnostic, so no prior scientific knowledge is required.

Course overview

This course is hands-on, with goal-oriented exercises structured to introduce information gradually.

You will execute several versions of a Nextflow pipeline that processes text inputs, starting with a simple single-step version and progressing to a multi-step version that takes a CSV file of inputs, runs a few transformation steps, and outputs a single text file containing ASCII art generated by a containerized tool.

This course focuses on running pipelines (named after the core nextflow run command). If you're looking for an intro to developing Nextflow pipelines, see Hello Nextflow.

Lesson plan

Course chapter Summary Estimated duration
Part 1: Run Nextflow Launch and manage Nextflow pipelines, understand essential workflow mechanics, and configure execution 45 mins

By the end of this course, you will be well-prepared for tackling the next steps in your journey to run reproducible workflows for your scientific computing needs.

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