Install VS Code

Visual Studio Code (VS Code) is a popular, free, and open-source code editor that supports Nextflow and nf-core pipeline development.

Installation

VS Code is available for Windows, macOS, and Linux. Download and install it from the official VS Code website.

Recommended extensions

Extensions enhance VS Code with additional features.

To install an extension:

1. Open VS Code
2. Select the Extensions icon in the left sidebar
3. Search for the extension name
4. Select Install

Nextflow extension

The official Nextflow extension provides comprehensive language support for Nextflow development, including:

• Syntax highlighting and validation
• Diagnostics and error detection
• Hover hints and documentation
• Code navigation (go to definition, find references)
• Intelligent code completion
• Code formatting
• Symbol renaming
• Parameter schema validation
• DAG (Directed Acyclic Graph) previews

This extension enforces Nextflow syntax standards and significantly improves your development workflow.

nf-core extension pack

The nf-core extension pack is a community-curated collection of useful tools for pipeline development and documentation:

• Apptainer/Singularity: Syntax highlighting for Apptainer/Singularity definition files
• Docker: Create, manage, and debug containerized applications
• EditorConfig: Maintain consistent coding standards across projects
• gitignore: Language support for .gitignore files
• Markdown Extended: Enhanced markdown previews with special formatting features
• Nextflow: Language support for Nextflow development
• Prettier: Code formatter using the Prettier tool
• Rainbow CSV: Highlight columns within CSV files with different colors
• Ruff: Extremely fast Python linter and code formatter, written in Rust
• Todo Tree: Shows TODO, FIXME, and similar comment tags in a tree view
• YAML: YAML language support with built-in Kubernetes syntax support

Remote development pack

For developers working with WSL, SSH, or containers, the Remote Development extension pack enables full VS Code functionality in remote environments. It includes:

• Remote - SSH: Connect to remote machines via SSH
• Dev Containers: Develop inside Docker containers
• WSL: Work seamlessly in Windows Subsystem for Linux

Other editors

While VS Code is widely used, several other editors also support Nextflow development:

Vim

Vim has official plugin support through the Nextflow language extension. Additional useful packages include:

• octo.nvim: Edit and review GitHub issues and pull requests directly within the editor
• kickstart.nvim: A documented, feature-rich configuration starter for Neovim

Emacs

An Emacs mode provides syntax highlighting for Nextflow code. Consider using Doom Emacs for a modular editor experience. Complementary packages include:

• Magit: Git management integrated into Emacs
• Forge: Extends Magit to work with GitHub and GitLab repositories

Sublime Text

Sublime Text benefits from a community-built plugin offering:

• Syntax highlighting compliant with DSL2
• Custom commands with integrations to external services
• Auto-completion and information panels
• Common code snippets

The plugin is available through package control.

Additional resources

For more information about installing install VS Code and other useful extensions, see:

• Nextflow environment setup