mkdocs.yml

site_name: bsbolt (BiSulfite Bolt)
repo_url: https://github.com/NuttyLogic/bsbolt
repo_name: 'GitHub'

theme:
  name: 'material'
  logo: img/lightning-bolt.png
  favicon: img/lightning-bolt.png

nav:
  - Home: index.md
  - Installation: installation.md
  - Alignment:
    - Index Generation: bsb_index.md
    - Read Alignment: align.md
    - Alignment Output: alignment_output.md
  - Methylation Calling: methylation_calling.md
  - Methylation Matrix Generation:
    - Matrix Assembly: matrix.md
    - Matrix Imputation: imputation.md
  - Simulation:
    - Simulation Background: sim_ref.md
    - Read Simulation: read_simulation.md
  - API:
    - Index: index_api.md
    - Align: align_api.md
    - Methylation Calling: meth_call_api.md
    - Matrix Assembly: matrix_api.md
    - Imputation: imputation_api.md
    - Simulation: simulation_api.md
    - Utilities: utils_api.md
    - Variant Calling: variant_api.md
  #- Tutorial: tutorial.md
  #- Pipelines: pipelines.md

markdown_extensions:
  - admonition
  - codehilite
  - mkautodoc

extra_css:
    - custom.css