mkdocs.yml

site_name: MeSS
repo_name: metagenlab/mess
repo_url: https://github.com/metagenlab/MeSS
site_author: Farid Chaabane
theme:
  name: material
  icon:
    logo: material/library-outline
    repo: fontawesome/brands/github
  palette:
    # Palette toggle for light mode
    - scheme: default
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Palette toggle for dark mode
    - scheme: slate
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  features:
    - navigation.instant
    - navigation.sections
    - navigation.prune
    - navigation.indexes
    - content.code.copy

markdown_extensions:
  - attr_list
  - md_in_html
  - def_list
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg
  - admonition
  - pymdownx.details
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format

  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.arithmatex:
        generic: true

extra_javascript:
  - javascripts/katex.js
  - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.js
  - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/contrib/auto-render.min.js

extra_css:
  - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.css


nav:
  - index.md
  - Motivation: motivation.md
  - Citation: citation.md
  - Getting started:
      - getting_started/index.md
      - Install: install.md
      - Step-by-step guide:
        - guide/index.md
        - 1) Setup inputs: guide/input.md
        - 2) Download genomes: guide/download.md
        - 3) Simulate reads: 
          - guide/simulate/index.md
          - a) Fasta processing: guide/simulate/fa-processing.md
          - b) Calculate coverage: guide/simulate/coverage.md
          - c) Read simulation and processing: guide/simulate/reads.md
        - 4) Examine outputs: guide/output.md
  - Commands:
    - commands/index.md
    - download: commands/download.md
    - simulate: commands/simulate.md
    - run: commands/run.md
    - hmp-template: commands/hmp-template.md
  - Tutorials:
    - tutorials/index.md
    - Taxonomic profiles as input:
      - tutorials/profilers/index.md
      - Kraken2: tutorials/profilers/kraken2.md
      - Bracken: tutorials/profilers/bracken.md
    - Sequencing technologies:
      - tutorials/seqtech/index.md
      - Illumina: tutorials/seqtech/illumina.md
      - Nanopore: tutorials/seqtech/nanopore.md
      - PacBio: tutorials/seqtech/pacbio.md
  - Benchmarks:
      - benchmarks/index.md
      - Species composition: benchmarks/species-composition.md
      - Resource usage: benchmarks/resource-usage.md