Hello Nextflowcourse¶
-
Course summary
Hello Nextflow is a hands-on introduction to building reproducible and scalable data analysis workflows.
Working through practical examples and guided exercises, you will learn the fundamentals of developing pipelines with Nextflow, including how to define processes, connect them into pipelines, manage files and software dependencies, parallelize execution effortlessly, and run workflows across different computing environments.
You will take away the skills and confidence to start developing and running your own workflows with Nextflow.
-
Additional information
Technical requirements
You will need a GitHub account OR a local installation of Nextflow. See Environment options for more details.
Learning objectives
- Launch and manage execution of Nextflow workflows
- Find and interpret outputs (results) and log files generated by Nextflow
- Troubleshoot basic issues
- Build a simple multi-step workflow from core Nextflow components
- Distinguish between essential types of channel factories and operators and utilize them effectively in a simple workflow
- Configure pipeline execution to run on common computing platforms including HPC and cloud
- Apply best practices for reproducibility, portability and code re-use that make pipelines FAIR, including code modularity and software containers
Audience & prerequisites
- Audience: This course is designed for learners who are completely new to Nextflow and want to develop their own pipelines.
- Skills: Some familiarity with the command line, basic scripting concepts and common file formats is assumed.
- Domain: The exercises are all domain-agnostic, so no prior scientific knowledge is required.
Course videos
Videos are available for each chapter, featuring an instructor working through the exercises. The video for each part of the course is embedded at the top of the corresponding page.
Course overview¶
This course is designed to be hands-on, with goal-oriented exercises structured to introduce information gradually.
You will develop a simple Nextflow pipeline that takes some text inputs, runs a few transformation steps, and outputs a single text file containing an ASCII picture of a character saying the transformed text.
Lesson plan¶
In order to avoid overwhelming you with concepts and code, we've broken this down into six parts that will each focus on specific aspects of developing pipelines with Nextflow.
| Course chapter | Summary | Estimated duration |
|---|---|---|
| Part 1: Hello World | Basic components and principles involved in assembling and running a Nextflow workflow | 30 mins |
| Part 2: Hello Channels | Using channels and operators for processing inputs and parallelizing execution effortlessly | 45 mins |
| Part 3: Hello Workflow | Using channels to chain multiple steps together and handle transfer of data between steps | 60 mins |
| Part 4: Hello Modules | Applying code modularity principles to increase reusability and decrease maintenance burden | 20 mins |
| Part 5: Hello Containers | Using containers as a mechanism for managing software dependencies and increase reproducibility | 60 mins |
| Part 6: Hello Config | Customizing pipeline behavior and optimizing usage in different computational environments usage | 60 mins |
By the end of this course, you will be well-prepared for tackling the next steps in your journey to develop reproducible workflows for your scientific computing needs.
Ready to take the course?