mkdocs.yml

site_name: Pypiper
site_logo: img/pypiper_logo_dark.svg
site_url: http://code.databio.org/pypiper/
repo_url: http://github.com/databio/pypiper
pypi_name: piper

nav:
  - Getting Started: 
    - Introduction: README.md
    - Philosophy: philosophy.md
    - Features at-a-glance: features.md
    - Hello world: hello-world.md
  - Developer guides:    
    - Building a basic pipeline: basic-pipeline.md
    - Using the run method: advanced-run-method.md
    - Automatic command-line arguments: cli.md
    - Configuring pipelines: configuration.md
    - Reporting statistics: report.md
    - Reporting statistics with pipestat: pipestat.md
    - Cleaning up intermediate files: clean.md
    - Best practices: best-practices.md
  - Toolkits:
    - "NGSTk: the NGS toolkit": ngstk_intro.md    
  - Reference:
    - Catalog of pipeline outputs: outputs.md
    - Pypiper API: autodoc_build/pypiper.md
    - NGSTk API: autodoc_build/ngstk.md
    - FAQ: faq.md
    - Support: support.md
    - Contributing: contributing.md
    - Changelog: changelog.md

theme: databio

plugins:
  - databio:
      autodoc_build: "docs/autodoc_build"
      autodoc_package: "pypiper"
      no_top_level: true
      build_list:
        pypiper: [PipelineManager]
        ngstk: [NGSTk]
  - search