Introduction¶
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!
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.
Prerequisites
- A GitHub account
- Experience with command line
- Experience writing pipelines with Nextflow