Nextflow Runcourse¶
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Course summary
Nextflow Run is a hands-on introduction to running reproducible and scalable data analysis workflows.
Working through practical examples and guided exercises, you will learn the fundamentals of using Nextflow, including how to execute 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 running workflows with Nextflow.
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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
- Troubleshoot basic issues
- Recognize core Nextflow components in a simple multi-step workflow
- Configure pipeline execution to run on common computing platforms including HPC and cloud
- Summarize 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 execute existing 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 overview¶
This course is designed to be hands-on, with goal-oriented exercises structured to introduce information gradually.
You will execute several versions of a Nextflow pipeline that processes text inputs. You'll start with a simple version that consists of a single step, and eventually progress to a multi-step version that takes a CSV file of tabular 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¶
We've broken this down into three parts that will each focus on specific aspects of running and managing pipelines written in Nextflow.
| Course chapter | Summary | Estimated duration |
|---|---|---|
| Part 1: Run basic operations | Launching and managing execution of a simple workflow | 30 mins |
| Part 2: Run real pipelines | Processing complex inputs, running multi-step workflows, using containers and parallelizing execution effortlessly | 60 mins |
| Part 3: Run configuration | Customizing pipeline behavior and optimizing usage in different computational environments | 60 mins |
By the end of this course, you will be well-prepared for tackling the next steps in your journey to run reproducible workflows for your scientific computing needs.
Ready to take the course?