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Nextflow Triathlon

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Our Training Collections provide curated learning paths through our training materials. This collection is a fast-track introduction to the Nextflow ecosystem, from running your first pipeline to launching production-scale workflows on Seqera Platform.

Learning objectives

By the end of this collection, you'll have experience with:

  • Running Nextflow pipelines — launching and managing execution, understanding channels, operators, and containers
  • Running nf-core pipelines — finding, retrieving, and configuring community pipelines
  • Running pipelines with Seqera Platform — launching and monitoring pipelines at scale, from the web interface and the CLI

These skills will enable you to run reproducible, scalable Nextflow workflows using both the command line and Seqera Platform.

Audience & prerequisites

This collection is designed for learners who are new to Nextflow and want a fast-track introduction covering the command line, nf-core, and Seqera Platform.

Prerequisites

  • Some familiarity with the command line, basic scripting concepts, and common file formats
  • No prior Nextflow, nf-core, or scientific domain experience is required

Collection contents

This collection consists of three parts that build on each other:

  1. Nextflow Run — Launch and manage Nextflow pipelines, understand essential workflow mechanics, and configure execution
  2. nf-core Run — Find, retrieve, and configure nf-core community pipelines, including a production-scale pipeline
  3. Running Pipelines with Seqera Platform — Launch and monitor pipelines with Seqera Platform, from the web interface and the CLI

We recommend completing them in the order listed above, since each part builds on the pipelines and skills introduced in the previous one.

How to use this collection

First, command-click on the "Open in GitHub Codespaces" button below to launch the training environment in a separate tab, then read on while it loads.

Open in GitHub Codespaces

Once your environment is running, work through the collection as follows:

  1. In this tab: Navigate to the first course listed above, which describes step-by-step exercises.
  2. In your Codespaces tab: Work through the exercises for that course.
  3. When you complete a course or side quest, return to this page and navigate to the next one in the list above.
  4. When you have completed the collection, click the button below to fill out a very short survey. Your feedback allows us to continue improving the training materials for everyone.

Take the survey

Ready to begin? Start with the first course above!