mkdocs.yaml

# Project Information
site_name: khanlab-NGS-Pipeline
site_author: Vineela Gangalapudi
site_description: >-
  The space will be used to provided documentation for khanlab NGS pipeline.

# Repository
repo_name: AWS_POC_MVP_NF
repo_url: https://github.com/CCRGeneticsBranch/Oncogenomics_NF_WF
edit_uri: https://github.com/CCRGeneticsBranch/Oncogenomics_NF_WF/edit

# Copyright
copyright: Copyright © 2022 CCR Genetics

# 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
#  logo: assets/images/doc-book.svg
#  favicon: assets/images/favicon.png

# 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/CCRGeneticsBranch
    - 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.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.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:
  - Overview: index.md
  - Setting up Samplesheet: samplesheet.md
  - Running the Pipeline: pipeline_launch.md
  - Pipeline References & Tools: references.md
  - Dockers: dockers.md