mkdocs.yml

site_name: Dahak Metagenomics
site_url: https://dahak-metagenomics.github.io/dahak
repo_name: dahak-metagenomics/dahak
repo_url: https://github.com/dahak-metagenomics/dahak
edit_uri: ""

# This is a boilerplate DIB Lab footer
# This will likely change...
copyright: 'Copyright &copy; 2017-2018, The Regents of the University of California.<br />
Written and maintained by the <a href="http://ivory.idyll.org/lab/">Lab for Data Intensive Biology</a> at UC Davis.<br />
Released under the <a href="https://opensource.org/licenses/BSD-3-Clause">BSD 3-Clause License</a>.<br /><br />'

# change directory names here
docs_dir: docs
site_dir: site

# give a title for each page
pages:
  - 'Index' : 'index.md'
  - 'Installing' : 'installing.md'
  - 'Workflows Overview' : 'workflows_overview.md'
  - 'Running Workflows' : 'running_workflows.md'
  - 'Workflow Configuration' : 'config.md'
  - 'Quick Start' : 'quickstart.md'
  - 'HPC Quick Start' : 'hpc_quickstart.md'
  - 'Troubleshooting' : 'troubleshooting.md'

  - 'Read Filtering':
    - 'Overview' : 'readfilt_overview.md'
    - 'Walkthrough' : 'readfilt_walkthru.md'
    - 'Snakemake' : 'readfilt_snakemake.md'

  - 'Assembly':
    - 'Overview' : 'assembly_overview.md'
    - 'Walkthrough' : 'assembly_walkthru.md'
    - 'Snakemake' : 'assembly_snakemake.md'

  - 'Comparison':
    - 'Overview' : 'comparison_overview.md'
    - 'Walkthrough' : 'comparison_walkthru.md'
    - 'Snakemake' : 'comparison_snakemake.md'

  - 'Taxonomic Classification':
    - 'Overview' : 'taxclass_overview.md'
    - 'Walkthrough' : 'taxclass_walkthru.md'
    - 'Snakemake' : 'taxclass_snakemake.md'

  - 'Contributing' : 'contrib.md'

theme:

  # use local theme
  name: null
  custom_dir: 'mkdocs-material-dib/material'

  # pretty colors! see https://squidfunk.github.io/mkdocs-material/getting-started/#primary-colors
  palette:
    primary: 'brown'
    accent: 'brown'
  
  # fun logos! see https://material.io/icons/
  logo:
    icon: 'line_style'

  font:
    text: 'Ubuntu'
    code: 'Ubuntu Mono'

# this will add docs/css/custom.css to all your docs
extra_css:
  - css/custom.css

# Extensions
markdown_extensions:
  - admonition
  - codehilite:
      guess_lang: false
  - toc:
      permalink: true