RENEE/mkdocs.yml at main · CCBR/RENEE · GitHub

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# Project Information
site_name: RENEE Documentation
site_author: CCBR
site_description: >-
  RENEE is an open-source, reproducible, and scalable best
  practices pipeline for analyzing RNA-sequencing data.

# Repository
repo_name: CCBR/RENEE
repo_url: https://github.com/CCBR/RENEE
edit_uri: https://github.com/CCBR/RENEE/edit/master/docs/

# Copyright
copyright: Copyright &copy; 2023-{{ now().year }} CCBR

# Configuration
theme:
  name: readthedocs
  locale: en
  custom_dir: docs/overrides
  #
# 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

extra_css:
  - css/custom.css
extra_javascript:
  - js/custom.js

# 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.caret
  - pymdownx.critic
  - pymdownx.details
  - pymdownx.highlight
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.snippets:
      check_paths: true
  - pymdownx.superfences
  - pymdownx.tabbed
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.tilde

# Page Tree
nav:
  - About: index.md
  - Theory: RNA-seq/Theory.md
  - Getting started: RNA-seq/TLDR-RNA-seq.md
  - Command Line:
      - run: RNA-seq/run.md
      - build: RNA-seq/build.md
      - cache: RNA-seq/cache.md
      - unlock: RNA-seq/unlock.md
  - Graphical Interface: RNA-seq/gui.md
  - Expected Output: RNA-seq/output.md
  - Resources: RNA-seq/Resources.md
  - FAQ:
      - General Questions: general-questions.md
      - Troubleshooting: troubleshooting.md
      - How to contribute: contributing.md
  - License: license.md