mkdocs.yml

# Project Information
site_name: PIPELINENAME Pipeline
site_author: Samantha Sevilla, Ph.D.
site_description: >-
  PIPELINENAME Pipeline
# Repository
repo_name: CCBR/PIPELINENAME
repo_url: https://github.com/CCBR/PIPELINENAME
edit_uri: https://github.com/CCBR/PIPELINENAME/edit/main/docs/

# Copyright
copyright: Copyright © 2022 CCBR

# Configuration
theme:
  name: material
  features:
    - navigation.tabs
    - navigation.top
    - navigation.indexes
    - toc.integrate 
  palette:
    - scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/toggle-switch-off-outline
        name: Switch to dark mode
    - scheme: slate
      primary: red
      accent: red
      toggle:
        icon: material/toggle-switch
        name: Switch to light mode

# Plugins
plugins:
  - search
  - git-revision-date
  - minify:
      minify_html: true


# Customization
extra:
  social:
    - icon: fontawesome/solid/users
      link: http://bioinformatics.cancer.gov
    - icon: fontawesome/brands/github
      link: https://github.com/CCBR
    - icon: fontawesome/brands/docker
      link: https://hub.docker.com/orgs/nciccbr/repositories
  version:
    provider: mike


# Extensions
markdown_extensions:
  - markdown.extensions.admonition
  - markdown.extensions.attr_list
  - markdown.extensions.md_in_html
  - markdown.extensions.def_list
  - markdown.extensions.footnotes
  - markdown.extensions.meta
  - markdown.extensions.toc:
      permalink: true
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.critic
  - pymdownx.details
  - pymdownx.emoji:
      emoji_index: !!python/name:materialx.emoji.twemoji
      emoji_generator: !!python/name:materialx.emoji.to_svg
  - pymdownx.highlight
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.magiclink:
      repo_url_shorthand: true
      user: squidfunk
      repo: mkdocs-material
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.snippets:
      check_paths: true
  - pymdownx.superfences
  - pymdownx.tabbed
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

# Page Tree
nav:
  - Background : index.md
  - Usage: 
    - 1. Getting Started : user-guide/getting-started.md
    - 2. Preparing Files: user-guide/preparing-files.md
    - 3. Running the Pipeline: user-guide/run.md
    - 4. Expected Output: user-guide/output.md
    - 5. Running Test Data: user-guide/test-info.md
  - FAQ:
    - Troubleshooting: user-guide/troubleshooting.md
    - Contributions: user-guide/contributions.md