mkdocs.yml

site_name: hCNV Reference Resources
site_description: 'Data & tools for hCNV analysis with a focus on the distributed normal'
site_author: Michael Baudis
repo_name: 'cnv-reference-resources'
repo_url: https://github.com/hCNV/cnv-reference-resources
edit_uri: edit/main/docs/

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nav:
  - Project Home: index.md
  - Input Data: data-resources.md
  - Parameters & Mappings: parameters-and-mappings.md
  - Beacon Queries: beacon-queries.md
  - MongoDB & Pymongo: mongodb-pymongo.md
  - hCNV Home: https://cnvar.org
  - VCF Data MongoDB: vcfdata-mongodb.md 

  - Biohack 2023 Page: https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/1
  - Beacon Documentation: 'https://docs.genomebeacons.org'

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markdown_extensions:
  - toc:
      toc_depth: 2-3
      permalink: true
  - admonition
  - attr_list
  - footnotes
  - md_in_html
  - pymdownx.critic
  - pymdownx.caret
  - pymdownx.details
  - pymdownx.keys
  - pymdownx.magiclink:
      hide_protocol: true
  - pymdownx.mark
  - pymdownx.tilde
  - pymdownx.saneheaders
  - pymdownx.snippets
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:mermaid2.fence_mermaid   
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tasklist:
      custom_checkbox: true
  - tables
  - mdx_gh_links:
      user: hCNV
      repo: cnv-reference-resources
  - pymdownx.emoji:
        emoji_index: !!python/name:materialx.emoji.twemoji
        emoji_generator: !!python/name:materialx.emoji.to_svg

###############################################################################

theme:
  name: material
  logo: img/hCNV-Elixir-logo.svg
plugins:
    - search
    - macros
    - mermaid2
extra_css:
  - css/theme_overrides.css