- Overview Test components with nf-test
- Assertions Write test assertions
- Advanced assertions Write complex assertions
- CI runners Configure RunsOn and fix CI disk space issues
Developing
Create and maintain nf-core pipelines, components, and configs
Overview
- Overview Develop nf-core pipelines
Testing
Components
- Automated methods Customize MultiQC methods descriptions
- Creating components Write modules and subworkflows
- Cross organisational components Use multi-organization modules
- Deprecating modules Deprecate a module or subworkflow
- ext arguments Configure tool-specific options
- Meta maps Using sample metadata stored in meta maps within nf-core pipelines
- Setting custom remotes Configure custom remotes
Containers
- ARM64 on Bioconda Enable ARM64 support for Bioconda packages
- Seqera Containers Use Seqera Containers
Documentation
- Harshil alignment Format Nextflow code for nf-core
- Style guide Follow nf-core style rules
- Topic types Understand documentation topic types
- Website Markdown Use special content elements
External use
- External use Use nf-core code externally
Institutional profiles
- Overview Write institutional profiles
- Configuration Structure institutional profile configuration
- Documentation Document institutional profiles
- File structure Create institutional profile files
- nf-core/configs outside nf-core Integrate profiles into custom workflows
- Preparing to write Prepare to write institutional profiles
- Testing Test institutional profiles
- Troubleshooting Troubleshoot institutional profiles
Migration guides
- Migrating to strict syntax Update nf-core/configs for Nextflow strict syntax compliance
- Migrating to topic channels Migrate to topic channels
Pipelines
- Adding modules Add modules to pipelines
- Release procedure A step-by-step guide for releasing a nf-core pipeline
- Renaming branches Switch default branch to main
- Template files Understand template elements
Template syncs
- Overview Keep pipelines up to date
- Fixing a broken TEMPLATE branch Fix a broken TEMPLATE branch
- Manually syncing your pipeline Sync pipeline with template manually
- Merging automated PRs Merge automated tool PRs
- Setting up a pipeline sync retrospectively Set up TEMPLATE branch
Tutorials
Writing nf-core modules
- Chapter 1: Introduction Learn to write nf-core modules
- Chapter 2: Getting started What you need before starting
- Chapter 3: What is a module? What defines an nf-core module
- Chapter 4: Boilerplate files How to generate the module file skeleton
- Chapter 5: Writing modules How to fill in the module files
- Chapter 6: Testing modules How to test an nf-core module
- Chapter 7: Development workflow How to contribute to the community
- Chapter 8: Using modules How to use nf-core modules in a pipeline