Data_UG.yml

---
#
# GDC Docs - Config
#

site_name: GDC Docs
site_url: https://docs.gdc.cancer.gov
repo_url: https://github.com/NCI-GDC/gdc-docs
copyright: '© 2015-2024'
nav:
  - GDC Data:
      - Introduction: Data/Introduction.md
      - GDC Data Model: Data/Data_Model/GDC_Data_Model.md
      - Data Security: Data/Data_Security/Data_Security.md
      - 'File Format: MAF': Data/File_Formats/MAF_Format.md
      - 'File Format: VCF': Data/File_Formats/VCF_Format.md
      - 'Bioinformatics Pipeline: DNA-Seq Analysis': Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline.md
      - 'Bioinformatics Pipeline: mRNA Analysis': Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline.md
      - 'Bioinformatics Pipeline: miRNA Analysis': Data/Bioinformatics_Pipelines/miRNA_Pipeline.md
      - 'Bioinformatics Pipeline: Copy Number Variation': Data/Bioinformatics_Pipelines/CNV_Pipeline.md
      - 'Bioinformatics Pipeline: Methylation Analysis': Data/Bioinformatics_Pipelines/Methylation_Pipeline.md
      - 'Bioinformatics Pipeline: Protein Expression': Data/Bioinformatics_Pipelines/RPPA_intro.md
      - Aligned Reads Summary Metrics: Data/Bioinformatics_Pipelines/Aligned_reads_summary_metrics.md
      - Release Notes: Data/Release_Notes/Data_Release_Notes.md
extra:
  project_root_dir: /
  project_org: GDC
  project_description: GDC Docs
  version: 1.0
theme:
  custom_dir: overrides
  favicon: images/favicon.ico
  features:
    - navigation.tabs
    - navigation.tabs.sticky
  logo: images/nih-header-logo-color.png
  name: material
  palette:
    primary: white
    scheme: gdc-accessible
markdown_extensions:
  - tables
  - pymdownx.superfences
  - pymdownx.tabbed:
      combine_header_slug: true
      alternate_style: true
      slugify: !!python/object/apply:pymdownx.slugs.slugify
        kwds:
          case: lower
  - pymdownx.details
plugins:
  - with-pdf:
      author: NCI GDC
      cover_title: GDC Data User's Guide
      cover_subtitle: NCI Genomic Data Commons (GDC)
      cover_logo: docs/images/nih-header-logo-color.png
      toc_level: 3
      exclude_pages:
        - ^$
      enabled_if_env: ENABLE_PDF_EXPORT
      render_js: false
      output_path: ../docs/Data/PDF/Data_UG.pdf