mkdocs.yml

theme: databio

site_name: PEPPRO
site_author: Jason Smith
site_url: http://peppro.databio.org/en/latest/
site_logo: img/peppro_logo_gray.svg
repo_url: https://github.com/databio/peppro/
#google_analytics: ['UA-127092878-1', 'code.databio.org/peppro']
paper_link: https://doi.org/10.1186/s13059-021-02349-4

markdown_extensions:
  - pymdownx.details  # pip install --user pymdown-extensions

nav:
  - Getting Started:
    - Introduction: 'README.md'
    - Features: 'features.md'
    - Install and run: 'install.md'
    - Extended tutorial: 'tutorial.md'
  - How-to Guides:
    - Run using bulker: 'run-bulker.md'
    - Run using containers: 'run-container.md'
    - Run using conda: 'run-conda.md'
    - Run natively: 'detailed-install.md'
    - Configure assets: 'assets.md'
    - Configure prealignments: 'prealignments.md'
    - Configure seqOutBias assets: 'sob.md'
    - Configure UMI: 'umi.md'
    - Configure custom adapters: 'custom_adapters.md'
    - Use custom reference data: 'annotation.md'
  - Reference: 
    - FAQ: 'faq.md'
    - Usage: 'usage.md'
    - Changelog: 'changelog.md'
    - Support: 'https://github.com/databio/peppro/issues'
    - PEPPRO paper output file structure: 'browse_output.md'
    - PEPPRO paper summary: 'files/examples/paper/PEPPRO_summary.html'

plugins:
  - search
  - databio:
      usage_template: "docs/usage_template.md"
      usage_cmds:
        -"$CODEBASE/databio/peppro/pipelines/peppro.py --help