Nextflow for Genomicscourse¶
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Resum del curs
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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.
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Informació addicional
Requisits tècnics
Necessitareu un compte de GitHub O una instal·lació local de Nextflow. Consulteu Opcions d'entorn per a més detalls.
Objectius d'aprenentatge
- 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
Públic i prerequisits
- 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.
Ready to take the course?