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Nextflow provides a powerful way to develop pipelines. However, it does not provide standards for how pipelines should be developed. This gap has led to the establishment of pipeline registries, such as nf-core, with tools and implementation guidelines that provide support and standards for pipeline development.

nf-core developed a base template to enable standardization and the adoption of good coding practices. The template establishes a pipeline file structure, with code, documentation, and continuous integration (CI) tests. The template plugs into the nf-core tooling, offering a full suite of commands that support pipeline usage and development.

Leveraging the nf-core template enables accelerated maintenance and development of pipelines.

Let's get started!

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Learning objectives

In this workshop, you will utilize the nf-core tooling to build a small pipeline using the nf-core template.

By the end of this workshop you will be able to:

  • Discuss the benefits of using the nf-core pipeline template
  • Identify the features of nf-core pipeline template that enable best practices
  • Add nf-core modules to a pipeline using the nf-core tooling
  • Add parameters to a pipeline and update the schema using the nf-core tooling

Audience & prerequisites

Please note that this is not a beginner's workshop and familiarity with Nextflow, the command line, and common file formats is assumed.


  • A GitHub account
  • Experience with command line
  • Experience writing pipelines with Nextflow