Use nf-corecourse¶
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Podsumowanie kursu
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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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Dodatkowe informacje
Wymagania techniczne
Będziesz potrzebować konta GitHub LUB lokalnej instalacji Nextflow'a. Szczegóły znajdziesz w Opcjach środowiska.
Cele szkoleniowe
- 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
Odbiorcy i wymagania wstępne
- 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 |
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| 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?