Prototype pipeline development container

Requirements

• VS Code ≥ 1.95
• Docker ≥ 24 (we recommend using Docker Desktop)

Configure Docker access

The simplest way of installing everything Docker is to use Docker Desktop. You can also go the engine way and install Docker manually.

Once installed, you need to configure some access rights to the Docker daemon. The easiest way to do this is to add your user to the docker group. This can be done with the following command :

sudo groupadd docker
sudo usermod -aG docker $USER

After running this command, you need to log out and log back in your terminal to apply the changes.

Usage

• Copy the devcontainer definition path at .devcontainer/prototyping and its content inside your project

  mkdir -p <project_dir>/.devcontainer
  cp -r .devcontainer/prototyping <project_dir>/.devcontainer/.
  

  • the target path in your project should be <project_dir>/.devcontainer/prototyping
• Open your project with VS CODE
  • create a new window with File > New Window or ctrl+shift+N, then use File > Open Folder.
• Click on the blue box in the lower left corner, to get a prompt to Reopen in container
  • alternatively, open the command palette with ctrl+shit+P and start typing Reopen in ... to filter in and select the command

The procedure will start a docker build, wait for a few minutes and enjoy your fully configured development environment.

Available in the container

• nf-core accessible through the terminal, which is configured to access nf-neuro modules and subworkflows
• git, github-cli
• curl, wget, apt-get
• nextflow, docker, tmux

Available in the VS Code IDE through extensions

• Docker images and containers management
• Nextflow execution environemnt
• Python and C++ linting, building and debugging tools
• Github Pull Requests management
• Github flavored markdown previewing
• Neuroimaging data viewer
• Test Data introspection
• Resource monitoring
• Remote development
• Live sharing with collaborators