SigProfilerMatrixGenerator/mkdocs.yml at master · SigProfilerSuite/SigProfilerMatrixGenerator · GitHub

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site_name: SigProfilerMatrixGenerator Documentation
site_description: Documentation for SigProfilerMatrixGenerator - a tool for generating mutational matrices
site_author: SigProfilerSuite
site_url: https://sigprofilersuite.github.io/SigProfilerMatrixGenerator/

repo_name: SigProfilerSuite/SigProfilerMatrixGenerator
repo_url: https://github.com/SigProfilerSuite/SigProfilerMatrixGenerator

docs_dir: docs

use_directory_urls: false

exclude_docs: |
  osf_wiki/**

theme:
  name: material
  palette:
    - scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.tabs
    - navigation.sections
    - navigation.expand
    - navigation.top
    - search.suggest
    - search.highlight
    - content.tabs.link
    - content.code.copy

plugins:
  - search

hooks:
  - mkdocs_hooks.py

markdown_extensions:
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - admonition
  - pymdownx.details
  - tables
  - attr_list
  - def_list
  - pymdownx.tasklist:
      custom_checkbox: true

nav:
  - Home: index.md
  - Getting Started:
    - Quick Start Example: Quick-Start-Example.md
  - Installation:
    - Python: Installation-Python.md
    - R: Installation-R.md
    - Supported Genomes: Currently-Supported-Genomes.md
  - Usage:
    - SBS, ID, DBS Input: Using-the-Tool-SBS-ID-DBS-Input.md
    - CNV Input: Using-the-Tool-CNV-Input.md
    - SV Input: Using-the-Tool-SV-Input.md
    - Output Overview: Using-the-Tool-Output.md
  - Output Reference:
    - CNV Output: Output-CNV.md
    - SBS Output: Output-SBS.md
    - DBS Output: Output-DBS.md
    - ID Output: Output-ID.md
    - TSB Output: Output-TSB.md
    - SV Output: Output-SV.md
    - VCF Files: Output-vcf_files.md
    - Plots: Output-Plots.md

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/SigProfilerSuite/SigProfilerMatrixGenerator

extra_css:
  - assets/stylesheets/extra.css