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Nextflow for Genomicscourse

  • Course summary

    A hands-on course applying Nextflow to a real-world genomics use case: variant calling with GATK.

    This course builds on the Hello Nextflow beginner training and demonstrates how to use Nextflow in the specific context of the genomics domain. You will implement a variant calling pipeline with GATK (Genome Analysis Toolkit), a widely used software package for analyzing high-throughput sequencing data.

  • 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. See Environment options for more details.

    Learning objectives
    • Write a linear workflow to apply variant calling to a single sample
    • Handle accessory files such as index files and reference genome resources appropriately
    • Leverage Nextflow's dataflow paradigm to parallelize per-sample variant calling
    • Implement multi-sample joint calling using relevant channel operators
    Audience & prerequisites
    • Audience: This course is designed for researchers in genomics and related fields who want to develop or customize data analysis pipelines.
    • Skills: Some familiarity with the command line, basic scripting concepts, and common genomics file formats is assumed.
    • Prerequisites: Foundational Nextflow concepts and tooling covered in Hello Nextflow.

Course overview

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

You will start by running the variant calling tools manually in the terminal to understand the methodology, then progressively build up a Nextflow pipeline that automates and scales the analysis.

Lesson plan

We've broken this down into three parts that each focus on specific aspects of applying Nextflow to a genomics use case.

Course chapter Summary Estimated duration
Part 1: Method overview Understanding the variant calling methodology and running the tools manually 30 mins
Part 2: Per-sample variant calling Building a pipeline that indexes BAM files and calls variants, then scaling to multiple samples 60 mins
Part 3: Joint calling on a cohort Adding multi-sample joint genotyping using channel operators to aggregate per-sample outputs 45 mins

By the end of this course, you will be able to apply foundational Nextflow concepts and tooling to a typical genomics use case.

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