mkdocs.yml

# Project
site_name: AACR Project GENIE Repository Documentation
site_description: >-
  This repository documents code used to gather, QC, standardize, and analyze data 
  uploaded by institutes participating in AACR's Project GENIE (Genomics, Evidence, 
  Neoplasia, Information, Exchange).
site_dir: docs_site

# Repository
repo_url: https://github.com/Sage-Bionetworks/Genie
repo_name: AACR Project GENIE

# Navigation
nav:
  - Home: index.md
  - Getting Started: getting_started.md
  - Tutorials: 
    - Local File Validation: tutorials/local_file_validation.md
  - Reference:
    # contains reference to all of the technical codebase
    - Main Pipeline Commands:
      # contains reference to the scripts with the command line args we call to 
      # run the pipeline
      - Input to Database: reference/main_pipeline_commands/input_to_database.md
      - Database to Staging: reference/main_pipeline_commands/database_to_staging.md
      - Consortium to Public: reference/main_pipeline_commands/consortium_to_public.md
    - Main Pipeline Steps:
      # contains all code related to input to database step
      - Input to Database:
        - input_to_database: reference/main_pipeline_steps/input_to_database/input_to_database.md
        - validate: reference/main_pipeline_steps/input_to_database/validate.md
        - write_invalid_reasons: reference/main_pipeline_steps/input_to_database/write_invalid_reasons.md
        - process_mutation: reference/main_pipeline_steps/input_to_database/process_mutation.md
        - to_retract: reference/main_pipeline_steps/input_to_database/toRetract.py
      - Database to Staging: reference/main_pipeline_steps/database_to_staging.md
      - Consortium to Public: reference/main_pipeline_steps/consortium_to_public.md
    - Fileformats:
      - Fileformat: reference/fileformats/fileformat.md
      - Assay Information: reference/fileformats/assay.md
      - Bed: reference/fileformats/bed.md
      - Clinical: reference/fileformats/clinical.md
      - Cna: reference/fileformats/cna.md
      - Maf: reference/fileformats/maf.md
      - Mutations In Cis: reference/fileformats/mutations_in_cis.md
      - Patient retraction: reference/fileformats/patient_retraction.md
      - Sample retraction: reference/fileformats/sample_retraction.md
      - Segmented: reference/fileformats/seg.md
      - Structural variant: reference/fileformats/structural_variant.md
      - Vcf: reference/fileformats/vcf.md
      - Workflow: reference/fileformats/workflow.md
    - Helper modules:
      # contains all code used in more than one step of the pipeline
      - create_case_lists: reference/helper_modules/create_case_lists.md
      - dashboard_table_updater: reference/helper_modules/dashboard_table_updater.md
      - extract: reference/helper_modules/extract.md
      - load: reference/helper_modules/load.md
      - process_functions: reference/helper_modules/process_functions.md
      - transform: reference/helper_modules/transform.md

# Theme configuration
theme:
  name: material
  features:
    - navigation.instant
    - navigation.tabs
    - search.highlight
    - search.share
    - toc.integrate
    - content.tabs.link
    - navigation.indexes
    - navigation.sections
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: green
      accent: green
      toggle:
        icon: material/weather-night
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: green
      accent: green
      toggle:
        icon: material/weather-sunny
        name: Switch to light mode
  # Enable the color mode toggle
  features:
    - content.code.copy
    - navigation.sections
    - navigation.tabs
    - navigation.top
    - navigation.tracking
    - navigation.instant
    - header.autohide
    - content.action.edit
    - content.tabs.link
    - content.tabs
    - search.highlight
    - search.share
    - search.suggest
    - toc.integrate
plugins:
- search
- autorefs
- mkdocstrings:
    default_handler: python
    handlers:
      python:
        options:
          members_order: source
          # shows all functions and attributes even hidden
          members: yes
          show_if_no_docstring: False
          show_root_heading: True
          show_root_full_path: True
          show_category_heading: True
          docstring_style: google
          docstring_section_style: spacy
          filters:
          - "!^_"
# Allows external links to open in a new tab
- open-in-new-tab

markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.superfences

  - toc:
      permalink: true