mkdocs.yml

# Please access https://squidfunk.github.io/mkdocs-material for more details.
site_name: Quartet Data Portal Docs
site_description: "Quality Control and Data Integration of Multi-omics Profiling"
site_author: "Jingcheng Yang"
announce: "Quartet Team"
announce_text: 'a development version has been released on <a href="https://dev.chinese-quartet.org" target="_blank">https://dev.chinese-quartet.org</a>'
docs_dir: docs/
repo_name: "chinese-quartet"
repo_url: "https://github.com/chinese-quartet"
edit_uri: docs.chinese-quartet.org/edit/master/docs/
markdown_extensions:
  - meta
  - abbr
  - admonition
  - pymdownx.details
  - attr_list
  - md_in_html
  - footnotes
  - toc:
      permalink: true
  - tables
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  - pymdownx.snippets
  - pymdownx.superfences
extra_css:
  - assets/stylesheets/extra.css
plugins:
  - search
  - git-revision-date
extra:
  homepage: https://chinese-quartet.org
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/chinese-quartet
      name: Chinese Quartet
  generator: false
copyright: Copyright &copy; 2016 - 2023 Quartet Team
theme:
  custom_dir: docs/assets/overrides
  features:
    - navigation.instant
    - navigation.tabs
    - navigation.tabs.sticky
    - navigation.top
    - search.highlight
    - search.suggest
    - search.share
  logo: assets/images/logo.png
  icon:
    repo: fontawesome/brands/github
  favicon: assets/images/logo.png
  palette:
    - scheme: default
      toggle:
        icon: material/toggle-switch-off-outline
        name: Switch to dark mode
      primary: blue
    - scheme: slate
      toggle:
      icon: material/toggle-switch-off-outline
      name: Switch to light mode
  name: "material"

# Table of contents
nav:
  - Home: index.md
  - "Getting Started":
      - Overview: getting_started/introduction.md
      - "Step by Step":
          - "Quality Assessment for WGS": getting_started/step_by_step_guide_dna.md
          - "Quality Assessment for Transcriptomics": getting_started/step_by_step_guide_rna.md
          - "Quality Assessment for Proteomics": getting_started/step_by_step_guide_protein.md
          - "Quality Assessment for Metabolomics": getting_started/step_by_step_guide_metabolite.md
      #  - Toolbars: getting_started/toolbars.md
      - "Register Account": getting_started/register_account.md
      - "Request Reference Materials": getting_started/request_reference_materials.md
      - "Access Quartet MultiOmics Data": getting_started/request_omics_data.md
      - "Submit Your Raw Omics Data": getting_started/submit_data.md
  # - 'Analyze Your Data':
  #   - 'Quality Assessment Page': getting_started/quality_assessment_page.md
  #   - 'Submit Data': getting_started/submit_data.md
  #   - 'Select Pipeline': getting_started/select_pipeline.md
  #   - 'Generate QC Report': getting_started/qc_report.md
  #   - 'Analysis History': getting_started/analysis_history.md
  # - 'Explore Reference Datasets':
  #   - 'Browser and Download': getting_started/browser_and_download.md
  #   - 'Interactive Visualization': getting_started/interactive_visualization.md
  - "Data & Pipelines":
      - Introduction: data_pipelines/intro.md
      - Genomics:
          - "Introduction": data_pipelines/genomics/intro.md
          - "Metadata Template": data_pipelines/genomics/metadata_template.md
          - "Omics Data Format": data_pipelines/genomics/omics_data_format.md
          - "Analysis Pipeline for WGS & WES": data_pipelines/genomics/analysis_pipeline.md
          # - 'QC Report': data_pipelines/genomics/qc_report.md
      - Transcriptomics:
          - "Introduction": data_pipelines/transcriptomics/intro.md
          - "Metadata Template": data_pipelines/transcriptomics/metadata_template.md
          - "Omics Data Format": data_pipelines/transcriptomics/omics_data_format.md
          - "Analysis Pipeline": data_pipelines/transcriptomics/analysis_pipeline.md
          - "QC Report": data_pipelines/transcriptomics/qc_report.md
      - Proteomics:
          - "QC Report": data_pipelines/proteomics/qc_report.md
          - "Sharing Raw Data": data_pipelines/proteomics/sharing_raw_data.md
      - Metabolomics:
          - "QC Report": data_pipelines/metabolomics/qc_report.md
          - "Sharing Raw Data": data_pipelines/metabolomics/sharing_raw_data.md
  - Tools:
      # - 'Data Repo': tools/data_repo.md
      - "Data Transfer Tools":
          - "OSSUtil": tools/ossutil.md
          - "OSSBrowser": tools/ossbrowser.md
  #  - 'Data Analysis Tools':
  #    - 'Choppy App': tools/choppy_apps.md
  #    - 'MultiReport': tools/multireport.md
  #  - 'Visualization Tools': tools/visualization_tools.md
  # - 'Data Dictionary':
  #   - About: data_dictionary/about.md
  #   - 'How to Prepare Your Metadata?': data_dictionary/metadata.md
  #   - 'Release Notes': data_dictionary/release_notes.md
  # - Roadmap:
  #  - Genomics: roadmap/genomics.md
  #  - Transcriptomics: roadmap/transcriptomics.md
  #  - Proteomics: roadmap/proteomics.md
  #  - Metabolomics: roadmap/metabolomics.md
  #  - Others: roadmap/others.md
  - Policies:
      - "Account Registration Policy": policies/account_registration_policy.md
      - "Reference Materials Policy": policies/reference_materials_policy.md
      - "Data Request Policy": policies/data_request_policy.md
      - "Data Submission Policy": policies/data_submission_policy.md
  - About:
      - News: about/news.md
      - Publications: about/publications.md
      #  - Quartet Team: about/members.md
      #  - Collaborators: about/collaborators.md
      - FAQs: about/faqs.md
  # - Developers:
  #   - News: developers/changelog.md