• Home
  • Pipelines
  • Resources
    • Components
    • Modules
    • Subworkflows

    • Configs
    • Shared configs

    • Plugins & Actions
    • nft-utils
    • setup-nextflow
    • setup-nf-test
  • Docs
  • Community
    • What's happening
    • Advisories
    • Blog

    • Events
    • Bytesize Talks
    • Hackathons
    • Training
    • Talks
    • Weekly Helpdesks

    • Programs and groups
    • Special interest groups
    • In-progress RFCs
    • Mentorships
    • Contributors
    • Shop new
    • Connect game 👾
  • About
    • About nf-core
    • Stickers
    • Governance
    • Marketing
    • Code of conduct

    • Publications
    • Statistics

    • Join nf-core
    • Select theme
    • Light
    • Dark
    • System
    • Select theme
    • Light
    • Dark
    • System
    Join nf-core Join nf-core
  1. Docs

Get started

New to nf-core? Start here to learn the basics and run your first pipeline.

What is nf-core?

What is nf-core?

Learn about nf-core

Environment setup

Overview

Set up your environment

Nextflow

Install Nextflow

Software dependencies

Manage software dependencies

nf-core tools

Install nf-core/tools

VS Code

Install VS Code and extensions

Dev Containers

Use and create Dev Containers

Troubleshooting

Troubleshoot common issues

Run your first pipeline

Run your first pipeline

Run your first pipeline

  • Get started
    • What is nf-core?
    • Environment setup
      • Overview
      • Nextflow
      • Software dependencies
      • nf-core tools
      • VS Code
      • Dev Containers
      • Troubleshooting
    • Run your first pipeline
  • Running
    • Overview
    • Advanced topics
      • Google Colab
      • Managing work directory growth
    • Configuration
      • Configuration options
      • System requirements
    • Reference genomes
    • Running pipelines
    • Running pipelines offline
  • Developing
    • Overview
    • Components
      • Automated methods
      • Creating components
      • Cross organisational components
      • Deprecating modules
      • ext arguments
      • Meta maps
      • Setting custom remotes
    • Containers
      • ARM64 on Bioconda
      • Seqera Containers
    • Documentation
      • Code formatting
      • Harshil alignment
      • Style guide
      • Topic types
      • Website Markdown
    • Institutional profiles
      • Overview
      • Configuration
      • Documentation
      • File structure
      • nf-core/configs outside nf-core
      • Preparing to write
      • Testing
    • Migration guides
      • Migrating to topic channels
    • Pipelines
      • Adding modules
      • External use
      • Release procedure
      • Renaming branches
      • Template files
    • Template syncs
      • Overview
      • Fixing a broken TEMPLATE branch
      • Manually syncing your pipeline
      • Merging automated PRs
      • Setting up a pipeline sync retrospectively
    • Testing
      • Overview
      • Advanced
      • Assertions
  • Contributing
    • Overview
    • Components
    • Contribution types
    • Contributor's list
    • Documentation
    • Existing pipelines
    • New pipelines
    • Project proposals
    • Reviewing pull requests
      • nf-core bot
      • Review checklists
        • Reviewing components
        • Reviewing nf-core/tools
        • 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
      • Overview
      • Recommendations
        • Publication credit
        • Testing
        • Bioconda
        • Build with community
        • Cloud compatible
        • Custom containers
        • DOIs
        • File formats
      • Requirements
        • Acknowledgements
        • CI testing
        • Community owned
        • Docker
        • Documentation
        • 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
    • Reviews
      • Overview
      • Request reviewers
      • Rapid merge
      • Review scope
      • Commit strategy
    • Test data
      • Overview
      • General
      • Modules
  • Community
    • Overview
    • Advisories
    • Brand
      • Overview
      • Colours
      • Fonts
      • Logos
      • Presentations
      • Workflow schematics
    • Governance
      • Core team tasks
      • Maintainers tasks
    • Regulatory
      • Overview
      • Checklist
    • Terminology
  • nf-core/tools
    • API
    • Cli
      • Installation
      • Pipelines
        • create
        • list
        • launch
        • create params file
        • download
        • licences
        • rocrate
        • lint
        • schema
        • bump version
        • sync
        • create logo
      • Modules
        • list
        • info
        • install
        • update
        • remove
        • patch
        • create
        • lint
        • test
        • bump versions
      • Subworkflows
        • list
        • info
        • install
        • update
        • remove
        • create
        • lint
        • test
      • Test datasets
        • list
        • list branches
        • search
      • TUI
Making awesome workflows since 2018.

Supported by:

+ + +
See the source code for this website on GitHub:
https://github.com/nf-core/website