This workshop provides an introduction to bioinformatics workflow managers, with a focus on Nextflow. Participants will gain an understanding of workflow management concepts and learn how to use Nextflow to develop scalable, reproducible, and portable bioinformatics pipelines. The session will include an overview of key features, practical examples, and guidance on best practices for implementing workflows in a research context. The workshop is designed for those interested in improving the efficiency and reproducibility of their computational biology analyses.
We assume some minimal exposure to GitHub and Nextflow. To get the most out of the workshop we would recommend participants look over the following training material beforehand:
- Software Carpentry's Git training
- Seqera's "Hello Nextflow" training
In terms of software/hardware requirements, everything can be run locally on your laptop or on HPC as you prefer. You will need Nextflow and nf-core tools installed and a container engine such as Docker or Singularity.
In this workshop you will learn:
- How to compose a bioinformatics workflow in Nextflow using a combination of writing your own modules and utilising the incredible nf-core modules resource.
- How to manipulate channels to move data through your workflow like a pro.
- How to implement logic switches in your pipeline.
- How to implement unit tests with nf-test.
- An appreciation of when writing a workflow might be a good idea, and how layers of additional complexity can make your workflow more flexible and robust.
Everything you need is in the docs/Lecture.html slides on the main branch. The lecture walks you through a series of tasks to build a toy pipeline. The solutions to the tasks are in sequentially numbered branches.
We'd love to hear if you implement our workshop and how it went! Drop us an email to tell us about it.
If you notice any mistakes, or would like to make a contribution please feel free to open an issue.