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Side Questscourse

  • Course summary

    Side Quests are standalone training mini-courses that go deeper into specific Nextflow topics.

    Each side quest can be taken independently, in any order, based on your interests and needs.

  • 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 EXCEPT the Hello nf-core course, which requires the v1 parser. See Environment options for more details.

    Learning objectives
    • Set up and configure a productive Nextflow development environment
    • Apply advanced scripting patterns for complex data transformations
    • Handle and propagate metadata through multi-step workflows
    • Split and group data channels for parallel and serial processing
    • Test Nextflow workflows using nf-test
    • Compose complex pipelines from reusable named workflow modules
    • Work efficiently with files using Nextflow file operations
    • Debug common workflow issues systematically
    • Use and build Nextflow plugins
    Audience & prerequisites
    • Audience: This collection is designed for learners who have completed the Hello Nextflow beginner course and want to go deeper into specific topics.
    • Skills: Experience with the command line and familiarity with basic Nextflow concepts and tooling is assumed.
    • Courses: Must have completed Hello Nextflow or equivalent.

Course overview

If this is your first time exploring the Side Quests, start with the Orientation page for an overview of the training environment and materials.

Side Quests

Side Quest Summary Time Estimate
Development Environment Set up and configure a productive local Nextflow development environment 45 mins
Essential Scripting Patterns Advanced scripting techniques for common workflow challenges 90 mins
File Input Processing File handling, path operations, and organizing outputs 45 mins
Metadata and Meta Maps Using metadata maps to track and propagate sample information 45 mins
Splitting and Grouping Techniques for splitting and regrouping data channels 45 mins
Testing with nf-test Writing and running tests for Nextflow workflows 1 hour
Troubleshooting Workflows Identifying and fixing common workflow errors 1 hour
Workflows of Workflows Composing complex pipelines from reusable named workflow modules 30 mins
Plugin Development Using and building Nextflow plugins 3 hours

Get started

Let us know what other topics you'd like to see covered here by posting in the Training section of the community forum.