Configuration

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Configuration of Devcontainers

nf-core repositories use pre-configured Devcontainers that can be run in GitHub Codespaces or locally with VS Code. These environments ensure all necessary software is available for developing and testing Nextflow pipelines and modules, while maintaining fast startup times.

The Devcontainer utilizes a pre-built custom Docker image (nfcore/devcontainer:latest). This image includes the core tools for nf-core development and various means to access further dependencies:

• Python
• nf-core tools
• Nextflow
• nf-test
• Apptainer
• Docker (via the docker-outside-of-docker feature using the host machine’s docker daemon)

VS Code extensions for Python, linting, and nf-core development are pre-installed.

The Devcontainer Configuration

The file .devcontainer/devcontainer.json is the main configuration manifest, which defines the environment, the base image, features, and more.

This example configuration file contains some key settings, similar to those used in nf-core repositories:

{
  "name": "nfcore",
 
  // Base image that installs:
  // nextflow, nf-test, tools, conda, apptainer
  "image": "nfcore/devcontainer:latest",
 
  // Run options for the container
  "remoteUser": "root",
 
  // Essential for running Apptainer (used with '-profile singularity')
  // Allows to perform the necessary mount operations within the container
  "privileged": true,
 
  // Executes the ./.devcontainer/setup.sh script after
  // the environment is created to perform final configuration
  "onCreateCommand": "./.devcontainer/setup.sh",
 
  // Install modular "plug-and-play" devcontainer features
  // Specifically the docker-outside-of-docker feature
  // (https://containers.dev/implementors/features/)
  "features": {
    "ghcr.io/devcontainers/features/docker-outside-of-docker:1.6.3": {}
  }
}

For a comprehensive list of settings see the relevant docs of the devcontainer specification

Customizing your Dev Container

You can further customize your environment by editing .devcontainer/devcontainer.json to add vs-code extensions, install additional tools, or adjust the environment. Common customizations include:

• Adding VS Code extensions for specific languages or linters
• Installing additional packages by modifying the setup.sh
• Integrate additional devcontainer features
• Adjusting resource requirements for local Devcontainers and Codespaces
• Mounting paths from the host machien when running locally

For more details, see the VS Code Dev Containers documentation.