.gitpod.yml

image: nfcore/gitpod:dev
tasks:
  - name: Update Nextflow and setup pre-commit
    command: |
      pre-commit install --install-hooks
      nextflow self-update
  - name: Install maven
    command: |
      conda install -y -c conda-forge maven
  - name: conda update
    command: |
      conda update --all --yes
  - name: unset JAVA_TOOL_OPTIONS
    command: |
      unset JAVA_TOOL_OPTIONS

vscode:
  extensions: # based on nf-core.nf-core-extensionpack
    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
    # - nextflow.nextflow                    # Nextflow syntax highlighting
    - oderwat.indent-rainbow # Highlight indentation level
    - streetsidesoftware.code-spell-checker # Spelling checker for source code
    - charliermarsh.ruff # Code linter Ruff