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Hello nf-core

nf-core is a community effort to develop and maintain a curated set of scientific pipelines built using Nextflow, as well as relevant tooling and guidelines that promote open development, testing, and peer review.

These pipelines are designed to be modular, scalable, and portable, allowing researchers to easily adapt and execute them using their own data and compute resources. The best practices guidelines enforced by the project further ensure that the pipelines are robust, well-documented, and validated against real-world datasets. This helps to increase the reliability and reproducibility of scientific analyses and ultimately enables researchers to accelerate their scientific discoveries.

nf-core is published in Nature Biotechnology: Nat Biotechnol 38, 276–278 (2020). Nature Biotechnology. An updated preprint is available at bioRxiv.

You can learn more about the project's origins and governance at https://nf-co.re/about.

During this training, you will be introduced to nf-core in a series of hands-on exercises.

Let's get started! Click on the "Open in GitHub Codespaces" button below to launch the training environment (preferably in a separate tab), then read on while it loads.

Open in GitHub Codespaces

Learning objectives

You will learn to use and develop nf-core compatible modules and pipelines, and utilize nf-core tooling effectively.

By the end of this training, you will be able to:

  • Find and run nf-core pipelines
  • Describe the code structure and project organization of nf-core pipelines
  • Create a basic nf-core compatible pipeline from a template
  • Convert basic Nextflow modules to nf-core compatible modules
  • Manage inputs and parameters using nf-core tooling
  • Add nf-core modules to an nf-core compatible pipeline

Audience & prerequisites

This is a general-purpose training for learners who have at least basic Nextflow skills and wish to level up to using nf-core.

Prerequisites

  • A GitHub account OR a local installation as described here.
  • Experience with command line and basic scripting.
  • Completed Hello Nextflow or equivalent.