mkdocs.yml

site_name: Tomahawk
repo_url: https://github.com/mklarqvist/tomahawk/
repo_name: 'GitHub'
site_author: Marcus D. R. Klarqvist
copyright: Copyright (C) 2016-present Genome Research Ltd., University of Cambridge, and Marcus D. R. Klarqvist
theme:
    name: material
    custom_dir: docs/material/
    logo: images/twk_logo_white.svg
extra_css:
  - 'stylesheets/extra.css'
extra_javascript:
  - 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-MML-AM_CHTML'

nav:
  - Home: index.md
  - Introduction: introduction.md
  - Installation: installation.md
  - Technical details:
    - Algorithm overview: algorithm-overview.md
    - Aggregation: aggregation.md
    - Job balancing: job-balancing.md
  - Tutorial:
    - CLI: tutorial.md
    - R: r-tutorial.md
    - Docker: docker-tutorial.md
  - Command line interface:
      - aggregate: cli/cli-aggregate.md
      - calc: cli/cli-calc.md
      - concat: cli/cli-concat.md
      - import: cli/cli-import.md
      - sort: cli/cli-sort.md
      - view: cli/cli-view.md
      - haplotype: cli/cli-haplotype.md
      - decay: cli/cli-decay.md
  - API documentation: api-documentation.md
  - Developer documentation: developer-documentation.md

markdown_extensions:
  - admonition
  - codehilite:
      linenums: true
  - toc:
      permalink: true