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  1. Docs

Guidelines

Overview of sections about Guidelines

This is the overview of the guidelines section.

Guidelines

Graphic design
    • Overview
    • Colours
    • Fonts
    • Logo
    • Presenting
    • Workflow diagrams
Pipelines
    • Overview
    • Recommendations
      • Bioconda
      • Build with community
      • Cloud compatible
      • Custom containers
      • DOIs
      • File formats
      • Publication credit
      • Testing
    • Requirements
      • Acknowledgements
      • CI testing
      • Community owned
      • Docker
      • Docs
      • Git branches
      • Identity branding
      • Keywords
      • Linting
      • Minimum inputs
      • MIT license
      • Nextflow
      • Parameters
      • RO Crate
      • Semantic versioning
      • Single command
      • Use the template
      • Workflow name
      • Workflow size
      • Workflow specificity
Regulatory
    • Overview
    • Checklist
Components
    • Overview
    • Modules
    • Subworkflows
    • Test data
    • Module deprecation
Documentation
    • Writing style
External use

Guidance on how to use nf-core code and best practices in non-nf-core pipelines.

Google slides progressbar
    • Overview
    • Privacy
    • Support
    • Terms of Service
Pull request review

Best practices to review contributions.

  • Checklists
    • Pipeline release
    • Reviews
      • Pipeline Release PR
      • Component PR
      • nf-core/tools PR
    • Community governance
      • Core team
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  • Contributing
    • Pipelines
      • Pipeline file structure
    • Software packaging
      • arm64 builds
    • nf-test
      • Assertions
    • Components
      • ext.args
      • Meta map
    • Website
      • Markdown
    • Code editors and styling
      • Code formatting
      • Editor plugins
      • Harshil alignment
    • Github
      • nf-core bot
    • How to contribute to nf-core
    • Project proposals
  • Guidelines
    • Graphic design
      • Overview
      • Colours
      • Fonts
      • Logo
      • Presenting
      • Workflow diagrams
    • Pipelines
      • Overview
      • Recommendations
        • Bioconda
        • Build with community
        • Cloud compatible
        • Custom containers
        • DOIs
        • File formats
        • Publication credit
        • Testing
      • Requirements
        • Acknowledgements
        • CI testing
        • Community owned
        • Docker
        • Docs
        • Git branches
        • Identity branding
        • Keywords
        • Linting
        • Minimum inputs
        • MIT license
        • Nextflow
        • Parameters
        • RO Crate
        • Semantic versioning
        • Single command
        • Use the template
        • Workflow name
        • Workflow size
        • Workflow specificity
    • Regulatory
      • Overview
      • Checklist
    • Components
      • Overview
      • Modules
      • Subworkflows
      • Test data
      • Module deprecation
    • Documentation
      • Writing style
    • External use
    • Google slides progressbar
      • Overview
      • Privacy
      • Support
      • Terms of Service
    • Pull request review
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    • Tests and test data
      • nf-test Comprehensive Guide
      • Components
        • 01 installation
        • 02 project setup
        • 03 testing modules
        • 04 testing subworkflows
      • Writing nf-test tests
      • Test data
      • Migrating to nf-test
    • nf-core components
      • Writing nf-core components
      • Adding modules to pipelines
      • Using seqera containers
      • Publish advisories
      • Writing automated methods descriptions
    • Pipelines
      • Switching master to main
    • Contributing to nf-core
      • Add your institution
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      • Writing training
    • External usage
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      • nf-core configs outside nf-core
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      • Creating with nf-core
      • Nextflow
    • nf-core training
      • Overview
      • Contributing training
        • nf-core contributing overview
      • Writing nf-core modules
        • Chapter 1: Introduction
        • Chapter 2: Setup
        • Chapter 3: What is a module?
        • Chapter 4: Boilerplate files
        • Chapter 5: Writing
        • Chapter 6: Testing
        • Chapter 7: Dev. Workflow
        • Chapter 8: Using
    • Sync
      • Overview
      • Fixing broken template branch
      • Manual sync
      • Merging automated prs
      • Sync retrospectively
  • Usage
    • Getting started
      • Introduction
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      • Offline
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    • Troubleshooting
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      • Early crash
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      • Retries
    • Reference genomes
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