Developing bioinformatics workflows with Nextflow
This workshop is designed to provide participants with a fundamental understanding of developing bioinformatics pipelines using nf-core templates.
Course Presenters
- Song Li, Bioinformatics Core Facility, Peter Mac
- Richard Lupat, Bioinformatics Core Facility, Peter Mac
Course Helpers
- Emma Gail, Melbourne Bioinformatics
- Sanduni Rajapaksa, Research Computing Facility, Peter Mac
- Adam Taranto, WEHI
- Alex Ringeri, WEHI
- Grace Hall, Melbourne Bioinformatics
Prerequisites
- Experience with command line interface and cluster/slurm
- Familiarity with the basic concept of workflows
- Attendance in the ‘Introduction to Nextflow and Running nf-core Workflows’ workshop, or an understanding of the Nextflow concepts outlined in the workshop material
Learning Objectives:
By the end of this workshop, participants should be able to:
- Learn the structure of nf-core templates
- Develop a basic Nextflow workflow using nf-core templates
- Re-use and import processes, modules, and sub-workflows into a Nextflow workflow
- Create custom modules using nf-core tools
- Define workflow logic within a workflow script
- Gain an understanding of pipeline version control
Set up requirements
Please complete the Setup Instructions before the course.
If you have any trouble, please get in contact with us ASAP via Slack.
Workshop schedule
| Lesson | Overview | Time |
|---|---|---|
| Session kick off | Session kick off: Discuss learning outcomes and finalise setup | 10.00 - 10.10 |
| Creating workflows using nf-core templates | Introduction to nf-core pipeline template structure and workflow syntax | 10.10 - 10.50 |
| Break | Break | 10:50 - 11:00 |
| nf-core modules and subworkflows | Installing/removing nf-core modules and subworkflows | 11.00 - 11:30 |
| Samplesheet parsing and nf-core modules | Working with nf-core modules | 11.30 - 12.15 |
| Lunch Break | Break | 12:15 - 13:00 |
| Module arguments and custom modules | Working with Nextflow-Schema & Metadata | 13.00 - 13.30 |
| Pipeline version control and additional resources | Pipeline development version control | 13.30 - 14:00 |
Credits and acknowledgement
This workshop is adapted from Fundamentals Training, Advanced Training, Developer Tutorials, and Nextflow Patterns materials from Nextflow and nf-core.