Reproducible bioinformatics workflows with Nextflow and nf-core¶
Nextflow is workflow management software that lets you write scalable, reproducible scientific workflows. It is widely used in bioinformatics for pipelines such as variant calling, RNA-seq, and metagenomics, and lets existing scripts in languages like R and Python be coupled together into a single workflow.
Nextflow integrates with common software packaging and environment management systems, including Docker, Apptainer, Conda, and environment modules. It simplifies running workflows on cloud and high-performance computing (HPC) infrastructures.
The workshop also covers nf-core, a community-driven project providing peer-reviewed, best-practice analysis pipelines built with Nextflow.
Trainers
Learning outcomes
By the end of this workshop you will be able to:
- Describe what Nextflow is and the problems it solves for bioinformatics workflows
- Run and inspect a Nextflow pipeline from the command line
- Explain what nf-core is and how its pipelines are structured
- Configure an nf-core pipeline for your own data and compute environment
- Apply best practices when running and sharing Nextflow pipelines
Prerequisites
- Familiarity with the Linux command line (navigating directories, running commands, editing files)
- No prior experience with Nextflow or nf-core is required
Setup¶
During this workshop, code will be run in real-time to demonstrate how Nextflow works. This will be run on the REANNZ OpenOnDemand platform which already has all the required software installed.
Acknowledgements¶
This workshop material was developed by Chris Hakkaart (Seqera) and Jen Reeve (REANNZ).