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Docs

Specifications

Overview of sections about Specifications

Specifications

Guidelines and requirements for nf-core contributions and best practices.

Components

Overview
Modules
Subworkflows

Pipelines

Overview
Recommendations
Requirements

Reviews

Overview
Request reviewers
Rapid merge
Review scope
Commit strategy

Test data

Overview
General
Modules

Get started
- What is nf-core?
- Environment setup
- Run your first pipeline
Running
- Overview
- Advanced topics
  - Google Colab
  - Managing work directory growth
- Configuration
  - Overview
  - System requirements
- Reference genomes
- Running pipelines offline
Developing
- Overview
- Components
- Containers
  - ARM64 on Bioconda
  - Seqera Containers
- Documentation
- Institutional profiles
- Migration guides
  - Migrating to topic channels
- Pipelines
- Template syncs
- Testing
Contributing
- Overview
- Components
- Contribution types
- Contributor's list
- Deprecating modules
- Documentation
- Existing pipelines
- New pipelines
- Project proposals
- Reviewing pull requests
  - nf-core bot
  - Review checklists
    
    Components
    nf-core/tools
    Pipelines
  - Reviewing pipeline releases
Specifications
- Overview
- Components
  - Overview
  - Modules
    
    General
    Naming conventions
    Input/output Options
    Documentation
    Parameters
    Resource requirements
    Software
    Testing
    Misc
  - Subworkflows
    
    General
    Naming conventions
    Input output options
    Subworkflow parameters
    Documentation
    Testing
    Misc
- Pipelines
- Reviews
- Test data
Community
- Advisories
- Brand
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  - Core team tasks
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- Regulatory
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- Terminology
nf-core/tools
- API
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  - Pipelines
    
    create
    list
    launch
    create params file
    download
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    create logo
  - Modules
    
    list
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    install
    update
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    patch
    create
    lint
    test
    bump versions
  - Subworkflows
    
    list
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    install
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  - Test datasets
    
    list
    list branches
    search
  - TUI

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