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nf-core Runcourse

  • Course summary

    nf-core Run is a hands-on introduction to finding, running, and configuring nf-core community pipelines.

    Working through practical examples and guided exercises, you will learn to find and retrieve nf-core pipelines, run them using their built-in test profiles, and customize their execution through parameters and configuration files.

    You will take away the skills and confidence to start running nf-core pipelines for your own analyses.

  • 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
    • Find, retrieve, and run nf-core community pipelines
    • Configure pipeline execution using parameters and configuration files
    • Understand how nf-core pipelines validate parameters and input data
    • Run a production-scale pipeline (nf-core/rnaseq) and override its default resource allocations
    Audience & prerequisites
    • Audience: This course is designed for learners who are new to Nextflow and nf-core and want to run existing community pipelines.
    • Skills: Some familiarity with the command line, basic scripting concepts and common file formats is assumed.
    • Domain: The exercises use bioinformatics pipelines, but no prior scientific domain knowledge is required.

Course overview

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

You will start with nf-core/demo, a minimal pipeline maintained by the nf-core project for training purposes, then apply what you've learned to nf-core/rnaseq, a widely-used production pipeline for bulk RNA sequencing analysis.

This course focuses on running pipelines. If you're looking for an intro to developing nf-core-compatible pipelines, see Hello nf-core.

Lesson plan

Course chapter Summary Estimated duration
Part 1: Run a demo pipeline Find and retrieve an nf-core pipeline, run it using its test profile, configure its execution, and run a production pipeline 60 mins

By the end of this course, you will be able to take advantage of the wealth of community pipelines offered by the nf-core project.

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