Nextflow workshop for beginners

This repository contains a small list of Nextflow-related branch-lessons for beginners. Each lesson is a different branch, so make sure to change branches incrementally. Each branch/lesson contains all required files, along with the command to execute. The point is to see step by step, how a Nextflow pipeline can be minimally built and then extended step-by-step.

Clone this repository on your local machine with the command git clone https://github.com/vagkaratzas/nextflow-beginners-workshop.git, open the downloaded directory with your favorite editor (highly recommend VS code), and fetch all branches/lessons with git fetch --all. If using VS code, make sure to download the Nextflow extension, that comes with language support for scripts and config files, enabling syntax highlighting, code navigation, formatting and more.

Make sure to install Nextflow by following the steps here. To check if Nextflow was installed correctly, execute the command nextflow -v. If you see the software's version, you can proceed!

Overview of lessons

• Lesson 1: Simple workflow with one module
• Lesson 2: Code organization in a clean architecture
• Lesson 3: Data chunking, the splitFasta operator
• Lesson 4: Running custom scripts, a python module example, and the collectFile operator
• Lesson 5: Containers and profiles
• Lesson 6: nf-core modules (gunzip), meta identifiers, map and flatten operators
• Lesson 7: Subworkflows, test and module configs

Switch to the Lesson-1 branch with git checkout Lesson-1 to begin.