- OverviewTest components with nf-test
- AssertionsWrite test assertions
- Advanced assertionsWrite complex assertions
- CI runnersConfigure RunsOn and fix CI disk space issues
Developing
Create and maintain nf-core pipelines, components, and configs
Overview
- OverviewDevelop nf-core pipelines
Testing
Components
- Automated methodsCustomize MultiQC methods descriptions
- Creating componentsWrite modules and subworkflows
- Cross organisational componentsUse multi-organization modules
- Deprecating modulesDeprecate a module or subworkflow
- ext argumentsConfigure tool-specific options
- GPU modulesWrite modules that use GPU acceleration
- Meta mapsUsing sample metadata stored in meta maps within nf-core pipelines
- Setting custom remotesConfigure custom remotes
Containers
- ARM64 on BiocondaEnable ARM64 support for Bioconda packages
- Seqera ContainersUse Seqera Containers
Documentation
- Harshil alignmentFormat Nextflow code for nf-core
- Style guideFollow nf-core style rules
- Topic typesUnderstand documentation topic types
- Website MarkdownUse special content elements
External use
- External useUse nf-core code externally
Institutional profiles
- OverviewWrite institutional profiles
- ConfigurationStructure institutional profile configuration
- DocumentationDocument institutional profiles
- File structureCreate institutional profile files
- nf-core/configs outside nf-coreIntegrate profiles into custom workflows
- Preparing to writePrepare to write institutional profiles
- TestingTest institutional profiles
- TroubleshootingTroubleshoot institutional profiles
Migration guides
- Migrating to strict syntaxUpdate nf-core/configs for Nextflow strict syntax compliance
- Migrating to topic channelsMigrate to topic channels
Pipelines
- Adding modulesAdd modules to pipelines
- Release procedureA step-by-step guide for releasing a nf-core pipeline
- Renaming branchesSwitch default branch to main
- Template filesUnderstand template elements
Template syncs
- OverviewKeep pipelines up to date
- Fixing a broken TEMPLATE branchFix a broken TEMPLATE branch
- Manually syncing your pipelineSync pipeline with template manually
- Merging automated PRsMerge automated tool PRs
- Setting up a pipeline sync retrospectivelySet up TEMPLATE branch
Tutorials
Writing nf-core modules
- Chapter 1: IntroductionLearn to write nf-core modules
- Chapter 2: Getting startedWhat you need before starting
- Chapter 3: What is a module?What defines an nf-core module
- Chapter 4: Boilerplate filesHow to generate the module file skeleton
- Chapter 5: Writing modulesHow to fill in the module files
- Chapter 6: Testing modulesHow to test an nf-core module
- Chapter 7: Development workflowHow to contribute to the community
- Chapter 8: Using modulesHow to use nf-core modules in a pipeline