mkdocs.yml

site_name: Introduction to NGS Workshop
site_description: This contains all material for the Introduction to NGS workshop.
site_author: Authors
docs_dir: modules

copyright: '© The authors; 2017-'

#Documentation and theme
theme: material

# Options
extra:
  palette:
    primary: 'indigo'
    accent: 'light blue'

  feature:
    tabs: false

  site_favicon: 'media/logos/Bioplatforms-Australia-favicon2.png'

markdown_extensions:
    - admonition
    - smarty
    - tables
    - markdown_include.include
    - codehilite
    - toc
    - mdx_math
    - pymdownx.betterem
    - pymdownx.caret
    - pymdownx.critic
    - pymdownx.inlinehilite
    - pymdownx.magiclink
    - pymdownx.mark
    - pymdownx.smartsymbols
    - pymdownx.superfences
    - pymdownx.tasklist
    - pymdownx.tilde
    - pymdownx.details

extra_css:
    #- css/extra.css
    - css/details.css

extra_javascript:
    - https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML
    - js/details.js

nav:
- Home: index.md
- The Trainers: trainers/trainers.md
- Workshop Information: preamble/preamble.md

- Hands-on Modules:
    - Introduction to Command Line: cli/handout/handout.md
    - Quality Control: qc/handout/handout.md
    - Read Alignment: alignment/handout/handout.md
    - RNA-Seq: rna-seq/handout/handout.md
    - De Novo Genome Assembly: denovo/handout/handout.md
    - De Novo Canu: denovo-canu/handout/handout.md
    - Eukaryote Genome Assembly: eukaryotic/handout/handout.md
    - Scaffolding: scaffolding/handout/handout.md

- License: license.md