Use nf-corecourse¶
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Course summary
Use nf-core is a hands-on introduction to finding, running, and configuring nf-core community pipelines.
Working through practical examples and guided exercises, you will learn to find and retrieve nf-core pipelines, run them using their built-in test profiles, and customize their execution through parameters and configuration files.
You will take away the skills and confidence to start running nf-core pipelines for your own analyses.
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Additional information
Technical requirements
You will need a GitHub account OR a local installation of Nextflow. Our training courses are compatible with Nextflow version 25.10.2 or later and require the use of the v2 parser. See Environment options for more details.
Learning objectives
- Find, retrieve, and run nf-core community pipelines
- Configure pipeline execution using parameters and configuration files
- Understand how nf-core pipelines validate parameters and input data
- Run a production-scale pipeline (nf-core/rnaseq) and override its default resource allocations
Audience & prerequisites
- Audience: This course is designed for learners who already know how to run local Nextflow pipelines and are new to nf-core, and want to run existing community pipelines.
- Skills: Some familiarity with the command line, basic scripting concepts and common file formats is assumed.
- Courses: Must have completed Nextflow Run or otherwise be comfortable running a local pipeline with
nextflow run. - Domain: The exercises use bioinformatics pipelines, but no prior scientific domain knowledge is required.
Course overview¶
This course is hands-on, with goal-oriented exercises structured to introduce information gradually.
You will start with nf-core/demo, a minimal pipeline maintained by the nf-core project for training purposes, then apply what you've learned to nf-core/rnaseq, a widely-used production pipeline for bulk RNA sequencing analysis.
This course focuses on running pipelines. If you're looking for an intro to developing nf-core-compatible pipelines, see Build with nf-core.
Lesson plan¶
| Course chapter | Summary | Estimated duration |
|---|---|---|
| Part 1: Run a demo pipeline | Find and retrieve an nf-core pipeline and run it using its test profile | 20 mins |
| Part 2: Configure pipeline execution | Set parameters, understand validation, and customize resource allocation and tool arguments | 20 mins |
| Part 3: Run a production pipeline | Pull and run nf-core/rnaseq, and override its default resource allocations | 20 mins |
By the end of this course, you will be able to take advantage of the wealth of community pipelines offered by the nf-core project.
Ready to take the course?