Welcome to the Nextflow Workshop! In this session, we will learn how to create automated, reproducible pipelines using Nextflow. Whether, you're new to bioinformatics or data science workflows or have some experience with other pipeline management systems, this workshop will guide you through the process of building a simple yet powerful pipeline.
- Basic UNIX coding skills
- Text editor (optional but highly recommended - VS Code)
In this workshop, we will cover the following key topics:
- Overview of Nextflow and how it helps automate data-science workflows.
- The importance of reproducibility and scalability in data-science.
- Introduction to workflow management systems (WFMS)
- A comparison between Snakemake and Nextflow: pros, cons, and when to choose one over the other
- How to set up a Nextflow environment and ensure all dependencies are installed.
- Instead of diving into a complex nextflow workflow, we'll start with a simple "Greetings" example.
- This mini-exercise will introduce you to the basics of creating a Nextflow script, defining processes, and understanding how data flows between steps.
- Instead of diving deep into bioinformatics or data-science, we'll use a fun, simple analogy: building a taco recipe 🌮🎉.
- Think of sequencing data as raw taco ingredients, processes like quality control and mapping as cooking, and the final results as assembling the tacos into a delicious outcome.
- Here, we will learn about parameters & variable, processes & channels, make modifications to the pipeline and make it scalable.
This workshop will introduce you to the fundamentals of Nextflow and demonstrate how to automate reproducible pipelines with ease. By the end of the session, you will be equipped to build, modify, and share your own bioinformatics or data science pipelines.
We hope you enjoy the workshop and that it sparks creativity in automating your own bioinformatics or data science pipelines! Happy Nextflow-ing! 🚀🎉