mkdocs.yml

# Project information
site_name:             'Zamanian Lab Docs'
site_description:      'An internal resource explaining and documenting lab pipelines'
site_author:           'Zamanian Lab'
site_url:              'https://zamanianlab.org/ZamanianLabDocs'


# Repository
repo_name:             'zamanianlab/ZamanianLabDocs'
repo_url:              'https://github.com/zamanianlab/ZamanianLabDocs'

# Configuration

extra_javascript:
  - 'javascripts/extra.js'
  - 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-MML-AM_CHTML'

extra_css:
  - stylesheets/extra_colors.css

theme:
  name: material
  language: en
  logo: images/dna.svg
  favicon: images/dna.svg
  palette:
    scheme: default
    primary: black
    accent: red
  font:
    text: Lato
    code: Roboto Mono
  features:
    - instant
  markdown_extensions:
    - admonition


# Remove footer
extra:
  generator: false

markdown_extensions:
  - attr_list
  - admonition
  - pymdownx.arithmatex
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.caret
  - pymdownx.critic
  - pymdownx.details
  - pymdownx.emoji:
      emoji_generator: !!python/name:pymdownx.emoji.to_svg
  - pymdownx.inlinehilite
  - pymdownx.magiclink
  - pymdownx.highlight
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.superfences
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde
  - pymdownx.tabbed

nav:
  - Home:                     index.md
  - Lab Manual:               labmanual.md
  - Protocols:            'protocols/protocols.md'
  - GDrive:                labgdrive.md
  - Computational Guide:
    - Overview:               comp_overview.md
    - Local Environment:      comp_local.md
    - Data Storage:           comp_storage.md
    - GitHub:                 comp_github.md
    - Conda:                  comp_conda.md
    - Homebrew:               comp_homebrew.md
  - Pipelines:
    - Overview:               pipelines_overview.md
    - Local Pipelines:        pipelines_local.md
    - Server Pipelines:       pipelines_server.md
    - Docker:                 pipelines_docker.md
    - wrmXpress Pipelines:    pipelines_wrmxpress.md