mkdocs.yml

site_name: SPAdes Assembly Toolkit

nav:
  - Home: index.md
  - Quick start: getting-started.md
  - Installation: installation.md
  - SPAdes input data:
    - Basic input: input.md
    - Hybrid assembly: hybrid.md
    - Tips on the parameters: datatypes.md
  - Command line options: running.md
  - SPAdes output: output.md
  - HMM-guided mode: hmm.md
  - Transcriptome assembly: rna.md
  - Binning refining: binspreader.md
  - HMM mapping on assembly graph: pathracer.md
  - Sequence to graph alignment: spaligner.md
  - SPAdes tools: standalone.md
  - Citation: citation.md
  - Feedback: feedback.md

use_directory_urls: false

theme:
  name: material
  logo: spades.png
  favicon: spades.png
  palette:
    primary: white
  features:
    - content.code.copy

markdown_extensions:
  - pymdownx.highlight:
      use_pygments: true
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
  - attr_list
  - md_in_html

plugins:
  - macros:
        module_name: docs/getversion