Developing bioinformatics workflows with Nextflow
This workshop is designed to provide participants with a fundamental understanding of developing bioinformatics pipelines using Nextflow. This workshop aims to provide participants with the necessary skills required to create a Nextflow pipeline from scratch or from the nf-core template.
Course Presenters
- Richard Lupat, Bioinformatics Core Facility
- Miriam Yeung, Cancer Genomics Translational Research Centre
- Song Li, Bioinformatics Core Facility
Course Helpers
- Sanduni Rajapaksa, Research Computing Facility
Prerequisites
- Experience with command line interface and cluster/slurm
- Familiarity with the basic concept of workflows
- Access to Peter Mac Cluster
- 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:
- Develop a basic Nextflow workflow consisting of processes that use multiple scripting languages
- Gain an understanding of Groovy and Nextflow syntax
- Read data of different types into a Nextflow workflow
- Output Nextflow process results to a predefined directory
- Re-use and import processes, modules, and sub-workflows into a Nextflow workflow
- Test and set up profiles for a Nextflow workflow
- Create conditional processes and conditional scripts within a process
- Gain an understanding of Nextflow channel operators
- Develop a basic Nextflow workflow with nf-core templates
- Troubleshoot known errors in workflow development
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/Teams.
Workshop schedule
| Lesson | Overview | Date |
|---|---|---|
| Setup | Follow these instructions to install VS Code and setup your workspace | Prior to workshop |
| Session kick off | Session kick off: Discuss learning outcomes and finalising workspace setup | Every week |
| Basic to Create a Nextflow Workflow | Introduction to nextflow channels, processes, data types and workflows | 29th May 2024 |
| Developing Modularised Workflows | Introduction to modules imports, sub-workflows, setting up test-profile, and common useful groovy functions | 5th Jun 2024 |
| Working with nf-core Templates | Introduction to developing nextflow workflow with nf-core templates | 12th Jun 2024 |
| Working with Nextflow Built-in Functions | operators | metadata | output-scatter-gather | Introduction to nextflow operators, metadata propagation, scatter, and gather | 19th Jun 2024 |
Credits and acknowledgement
This workshop is adapted from Fundamentals Training, Advanced Training, Developer Tutorials, and Nextflow Patterns materials from Nextflow and nf-core.