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mkdocs.yml
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site_name: Genomics Aotearoa AGM Training Workshop
site_author: GA & NeSI
site_dir: public
site_url: "https://genomicsaotearoa.github.io/AGM-workshop-2023/"
#Repository information
repo_name: GenomicsAotearoa/AGM-workshop-2023
repo_url: https://github.com/GenomicsAotearoa/AGM-workshop-2023
nav:
- Home: index.md
- Setup:
- setup/setup.md
- session_1/0_kickoff.md
- Session 1:
- session_1/1_introToNextflow.md
- Session 2:
- session_2/0_sessionOverview.md
- session_2/1_introTo_nfCore.md
- session_2/2_pipelineStructure.md
- session_2/3_sarekPipeline.md
- session_2/4_runConfiguration.md
- Session 3:
- session_3/0_homeStretchOverview.md
- session_3/1_configFiles.md
- session_3/2_configuration.md
- Appendix:
- session_3/3_appendix.md
theme:
name: material
custom_dir: ./overrides
logo: images/nesi_ga.png
favicon: images/nesi_ga.png
# 404 page
static_templates:
- 404.html
palette:
# Palette toggle for automatic mode
- media: "(prefers-color-scheme)"
toggle:
icon: material/brightness-auto
name: Switch to light mode
primary: custom
# Palette toggle for light mode
- media: "(prefers-color-scheme: light)"
scheme: default
primary: custom
toggle:
icon: material/brightness-7
name: Switch to dark mode
# Palette toggle for dark mode
- media: "(prefers-color-scheme: dark)"
scheme: slate
toggle:
icon: material/brightness-4
name: Switch to system preference
primary: custom
features:
- navigation.tracking
- navigation.sections
- navigation.expand
- navigation.top
- navigation.footer
- content.code.copy
- content.code.annotate
# Necessary for search to work properly
include_search_page: false
search_index_only: true
# Default values, taken from mkdocs_theme.yml
language: en
font:
text: Mukta
code: Fira Code
markdown_extensions:
- abbr
- admonition
- attr_list
- def_list
- footnotes
- meta
- md_in_html
- toc:
permalink: true
- pymdownx.arithmatex:
generic: true
- pymdownx.betterem:
smart_enable: all
- pymdownx.caret
- pymdownx.details
- pymdownx.emoji:
emoji_generator: !!python/name:materialx.emoji.to_svg
emoji_index: !!python/name:materialx.emoji.twemoji
- pymdownx.highlight:
anchor_linenums: true
- pymdownx.inlinehilite
- pymdownx.keys
- pymdownx.magiclink:
repo_url_shorthand: true
user: squidfunk
repo: mkdocs-material
- pymdownx.mark
- pymdownx.smartsymbols
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
- pymdownx.tabbed:
alternate_style: true
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.tilde
- pymdownx.snippets
plugins:
# - glightbox:
# effect: zoom
# zoomable: true
- search:
lang: en
extra_javascript:
- javascripts/mathjax.js
- https://polyfill.io/v3/polyfill.min.js?features=es6
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
copyright : Reproducible Bioinformatics Workflows with Nextflow and nf-core is licensed under a <a rel="noopener" target="_blank" href="https://www.gnu.org/licenses/gpl-3.0.en.html">GNU General Public License v3.0</a>
extra_css:
- stylesheets/extra.css