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mkdocs.yml
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mkdocs.yml
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site_name: ReCoDE RNA-seq Analysis
# Steps to follow on GitHub to publish your mkdocs site:
# 1. Create a new branch called gh-pages
# 2. Ensure GitHub Pages is enabled for your repository, Settings>Pages> Enable.
# Make sure that Source is set to `gh-pages` and `/(root)`. Save this setting.
# 3. Ensure that on GitHub workflows have read and write access to your repository
# Settings>Actions>General>Workflow permissions, tick `Read and write permissions`
# and save this setting.
# Change this to the name of your repo
repo_url: https://github.com/ImperialCollegeLondon/ReCoDE_rnaseq_pipeline
edit_uri: tree/main/docs/
theme:
name: material
custom_dir: docs
icon:
logo: logos/iclogo
favicon: assets/iclogo.png
font:
text: Roboto
code: Roboto Mono
palette:
- scheme: default
toggle:
icon: material/toggle-switch
name: Switch to dark mode
- scheme: slate
toggle:
icon: material/toggle-switch-off-outline
name: Switch to light mode
# SPA behaviour
features:
- navigation.instant
- navigation.top
- toc.follow
- content.code.annotate
extra:
homepage: https://imperialcollegelondon.github.io/ReCoDE-home/
nav:
- "index.md"
- Simple Pipeline - Background: "background_simple_local_pipeline.md"
- Simple Pipeline - Running: "running_simple_local_pipeline.md"
- Parallelised Pipeline - Background: "background_parallelised_pipeline.md"
- Parallelised Pipeline - Running: "running_parallelised_pipeline.md"
- Nextflow Pipeline - Background: "background_nextflow_pipeline.md"
- Nextflow Pipeline - Running: "running_nextflow_pipeline.md"
- "downstream_analysis.md"
# Add here all the plugins you want to use.
# Don't forget to add them in requirements.txt as well.
plugins:
- tags
- search
- include-markdown # https://github.com/mondeja/mkdocs-include-markdown-plugin
# Set settings for markdown extensions
markdown_extensions:
- meta
- mdx_math:
enable_dollar_delimiter: True
- pymdownx.highlight:
anchor_linenums: false
- pymdownx.inlinehilite
- pymdownx.snippets
- pymdownx.superfences
# Render math in mkdocs
extra_javascript:
- https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS_HTML