mkdocs.yml

site_name: "Cloudgene"
copyright: "© 2010 - 2024 Lukas Forer and Sebastian Schönherr"
repo_url: https://github.com/genepi/cloudgene3/
repo_name: genepi/cloudgene3

theme:
  name: material
  features:
    - content.tooltips
    #- navigation.expand
    - navigation.tabs
    #- navigation.tabs.sticky
    - search.highlight
    - search.share
    - search.suggest
    - toc.follow
    #- toc.integrate
    - content.tabs.link
    - content.code.annotate
    - content.code.copy
  font:
    text: Segoe UI #Avenir
    code: Roboto Mono

  palette:
    primary: blue
    accent: blue
  logo: "https://www.cloudgene.io/images/logo.png"
  favicon: images/favicon.svg

extra_css:
  - stylesheets/extra.css

extra_javascript:
  - https://buttons.github.io/buttons.js


nav:

- Home: index.md
- Installation: installation.md
- Documentation:
  - Getting Started: server/getting-started.md
  - Install Applications: server/install-apps.md
  - Manage Permissions: server/permissions.md
  - Manage Jobs: server/jobs.md
  - Configuration: server/configuration.md
  - Configure Nextflow: server/configure-nextflow.md
  - Customization: server/customization.md
  - Administration: server/administration.md
  - Develop Applications:
    - Getting Started: developers/introduction.md
    - Inputs: developers/inputs.md
    - Outputs: developers/outputs.md
    - Environment Variables: developers/environment_variables.md
    - Datasets: developers/datasets.md
    - Reporting: developers/reporting.md
  - Command Line Interface (CLI):
    - cloudgene install: cli/cloudgene-install.md
    - cloudgene github-install: cli/cloudgene-github-install.md
    - cloudgene clone: cli/cloudgene-clone.md
    - cloudgene remove: cli/cloudgene-remove.md
    - cloudgene ls: cli/cloudgene-ls.md
    - cloudgene validate: cli/cloudgene-validate.md
    - cloudgene run: cli/cloudgene-run.md
    - cloudgene server: cli/cloudgene-server.md
    - cloudgene version: cli/cloudgene-version.md
  - REST API Reference:
    - Getting Started: api/introduction.md
    - Authentication: api/authentication.md
    - Submit Job: api/job-submission.md
    - Job Status: api/job-status.md
    - List Jobs: api/list-jobs.md
    - Job Details: api/job-details.md
- About: about.md

markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.emoji:
      emoji_index: !!python/name:materialx.emoji.twemoji
      emoji_generator: !!python/name:materialx.emoji.to_svg
  - attr_list
  - md_in_html
  - toc:
      title: On this page
      permalink: true