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mkdocs.yml
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mkdocs.yml
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# Project Information
site_name: RENEE Documentation
site_author: CCBR
site_description: >-
RENEE is an open-source, reproducible, and scalable best
practices pipeline for analyzing RNA-sequencing data.
# Repository
repo_name: CCBR/RENEE
repo_url: https://github.com/CCBR/RENEE
edit_uri: https://github.com/CCBR/RENEE/edit/master/docs/
# Copyright
copyright: Copyright © 2023 CCBR
# Configuration
theme:
name: material
features:
- navigation.tabs
- navigation.top
- toc.integrate
palette:
- scheme: default
primary: indigo
accent: indigo
toggle:
icon: material/toggle-switch-off-outline
name: Switch to dark mode
- scheme: slate
primary: red
accent: red
toggle:
icon: material/toggle-switch
name: Switch to light mode
logo: assets/icons/doc-book.svg
favicon: assets/favicon/favicon.ico
# Plugins
plugins:
- search
- git-revision-date
- minify:
minify_html: true
- mike:
alias_type: symlink
canonical_version: latest
version_selector: true
# Customization
extra:
social:
- icon: fontawesome/solid/users
link: http://bioinformatics.cancer.gov
- icon: fontawesome/brands/github
link: https://github.com/CCBR
- icon: fontawesome/brands/docker
link: https://hub.docker.com/orgs/nciccbr/repositories
version:
provider: mike
# Extensions
markdown_extensions:
- markdown.extensions.admonition
- markdown.extensions.attr_list
- markdown.extensions.def_list
- markdown.extensions.footnotes
- markdown.extensions.meta
- markdown.extensions.toc:
permalink: true
- pymdownx.arithmatex:
generic: true
- pymdownx.caret
- pymdownx.critic
- pymdownx.details
- pymdownx.emoji:
emoji_index: !!python/name:materialx.emoji.twemoji
emoji_generator: !!python/name:materialx.emoji.to_svg
- pymdownx.highlight
- pymdownx.inlinehilite
- pymdownx.keys
- pymdownx.magiclink:
repo_url_shorthand: true
user: squidfunk
repo: mkdocs-material
- pymdownx.mark
- pymdownx.smartsymbols
- pymdownx.snippets:
check_paths: true
- pymdownx.superfences
- pymdownx.tabbed
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.tilde
# Page Tree
nav:
- About: index.md
- Theory: RNA-seq/Theory.md
- Getting started: RNA-seq/TLDR-RNA-seq.md
- Command Line:
- run: RNA-seq/run.md
- build: RNA-seq/build.md
- cache: RNA-seq/cache.md
- unlock: RNA-seq/unlock.md
- Graphical Interface: RNA-seq/gui.md
- Expected Output: RNA-seq/output.md
- Resources: RNA-seq/Resources.md
- FAQ:
- General Questions: general-questions.md
- Troubleshooting: troubleshooting.md
- How to contribute: contributing.md
- License: license.md