Overview

This comprehensive guide covers testing nf-core components using nf-test. This guide provides everything needed to create robust, maintainable tests for modules, subworkflows, and pipelines, from writing your first test to implementing advanced patterns.

Guide structure

Getting started

  1. Installation - Setting up nf-test in your development environment
  2. Project setup - Configuring your nf-core pipeline repository for testing with nf-test

Component Testing

  1. Testing modules - Testing individual nf-core modules
  2. Testing subworkflows - Testing nf-core subworkflows
  3. Testing pipelines - End-to-end pipeline testing

Data management and integration

  1. Test data management - Organizing and managing test datasets
  2. CI/CD integration - Integrating nf-test with continuous integration

Commands and reference

  1. nf-test commands and integration - Essential commands and nf-core integration

Troubleshooting & Best Practices

  1. FAQ and Debugging - Best practices, common issues, and solutions for nf-test

nf-core testing principles

nf-core testing follows these key principles:

  1. Comprehensive coverage: Every module, subworkflow, and pipeline should have tests
  2. Efficient test data: Tests use small, centralized datasets from nf-core/test-datasets
  3. Snapshot testing: Output verification through snapshots ensures consistency
  4. CI/CD ready: Tests run reliably in automated environments
  5. Standard patterns: Consistent testing patterns across all nf-core components

Getting help

For issues not covered in this guide:

Ready to get started? Begin with Installation to set up nf-test in your development environment.
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