Welcome to the Nextflow Crash Course, a series of hands-on workshops introducing pipeline development and execution with Nextflow.
Who this course is for
You’re comfortable on the command line and have written a bash script or two, but Nextflow is new to you. By the end of the workshop, you’ll have built a modular, multi-step DSL2 pipeline and run it on the Hazel cluster using SLURM and Apptainer containers.
Course at a glance
Day 0 · Prerequisites
Self-paced, before the workshop
Get set up on Hazel: logging in, navigating the filesystem, loading BRC modules, submitting SLURM jobs, and using Git on the cluster.
Day 1 · Thinking in Channels and Processes
Nextflow fundamentals
Your first process, building channels with channel factories and operators, and chaining processes into a FastQC + trimming workflow.
Day 2 · From Pipeline to Production
Config, modules, containers, and the cluster
Params, nextflow.config, and profiles; modular processes with include; Apptainer containers; SLURM execution; and a read-assembly capstone.
Work through the Day 0 material before Day 1. The workshop assumes you can log in, load modules, and submit a SLURM job.
After the workshop
Next Steps & Extra Material has where to go next, including nf-core and nf-test.
Additional resources
- COS Compute Handbook: general computing guide for College of Sciences users
- Hazel Crash Course: deeper introduction to the Hazel cluster