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mkdocs.yml
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mkdocs.yml
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# pip install pygments mkdocs-material pymdown-extensions
site_name: Bactopia
site_author: Robert A. Petit III
site_description: An extensive workflow to process Nanopore and Illumina sequencing for bacterial genomes.
copyright: >
Copyright © 2019-2024 Robert A. Petit III. All rights reserved. <a href="#__consent">Change Cookie Settings</a>
site_url: https://bactopia.github.io/
repo_url: https://github.com/bactopia/bactopia
dev_addr: 0.0.0.0:8000
theme:
name: material
custom_dir: overrides
palette:
- media: "(prefers-color-scheme)"
toggle:
icon: material/brightness-auto
name: Switch to light mode
- media: "(prefers-color-scheme: light)"
scheme: default
primary: teal
accent: teal
toggle:
icon: material/brightness-7
name: Switch to dark mode
- media: "(prefers-color-scheme: dark)"
scheme: slate
primary: deep purple
accent: deep purple
toggle:
icon: material/brightness-4
name: Switch to system preference
favicon: assets/favicon.ico
logo: assets/bactopia-small-logo.png
font:
text: 'Ubuntu'
code: 'Ubuntu Mono'
features:
- announce.dismiss
- content.action.edit
- content.code.copy
- navigation.footer
- navigation.instant
- navigation.instant.prefetch
- navigation.tabs
- navigation.tabs.sticky
- navigation.tracking
- navigation.top
plugins:
- blog:
archive: false
post_date_format: medium
post_url_date_format: yyyy
post_excerpt: optional
- privacy
- search:
lang: en
- social:
enabled: true
cache: true
cards: true
extra:
analytics:
provider: google
property: G-QH76FN9N78
social:
- icon: fontawesome/brands/github
link: https://github.com/bactopia/bactopia
- icon: fontawesome/brands/twitter
link: https://twitter.com/rpetit3
version:
provider: mike
consent:
title: Cookie Consent
description: >-
We use cookies to recognize your repeated visits and preferences, as well
as to measure the effectiveness of our documentation and whether users
find what they're searching for. With your consent, you're helping us to
make our documentation better.
extra_css:
- custom/magnific-popup.css
- custom/extra.css
extra_javascript:
- custom/fontawesome.js
- custom/jquery.min.js
- custom/jquery.magnific-popup.min.js
- custom/extra.js
markdown_extensions:
- admonition
- abbr
- 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_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- pymdownx.highlight:
anchor_linenums: true
line_spans: __span
pygments_lang_class: 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-experimental
format: !!python/name:pymdownx.superfences.fence_code_format
- pymdownx.tabbed:
alternate_style: true
- pymdownx.tasklist:
custom_checkbox: true
- pymdownx.tilde
nav:
- 'Bactopia':
- 'Introduction': 'index.md'
- 'Quick Start': 'quick-start.md'
- 'Installation': 'installation.md'
- "Beginner's Guide": 'beginners-guide.md'
- 'Tutorial': 'tutorial.md'
- 'Workflow Steps':
- 'Gather': 'bactopia/gather.md'
- 'QC': 'bactopia/qc.md'
- 'Assembler': 'bactopia/assembler.md'
- 'Annotator':
- 'Prokka': 'bactopia/annotator/prokka.md'
- 'Bakta': 'bactopia/annotator/bakta.md'
- 'Sketcher': 'bactopia/sketcher.md'
- 'Sequence Typing': 'bactopia/sequence-typing/mlst.md'
- 'Antimicrobial Resistance': 'bactopia/antimicrobial-resistance/amrfinderplus.md'
- 'Merlin': 'bactopia/merlin.md'
- 'Full Guide': 'full-guide.md'
# - 'Troubleshooting': 'troubleshooting.md'
- 'Changelog': 'changelog.md'
- 'Bactopia Tools':
- 'Introduction': 'bactopia-tools/index.md'
- 'Subworkflows':
- 'ariba': 'bactopia-tools/ariba.md'
- 'bakta': 'bactopia-tools/bakta.md'
- 'eggnog': 'bactopia-tools/eggnog.md'
- 'gtdb': 'bactopia-tools/gtdb.md'
- 'mashtree': 'bactopia-tools/mashtree.md'
- 'merlin': 'bactopia-tools/merlin.md'
- 'pangenome': 'bactopia-tools/pangenome.md'
- 'scrubber': 'bactopia-tools/scrubber.md'
- 'snippy': 'bactopia-tools/snippy.md'
- 'staphtyper': 'bactopia-tools/staphtyper.md'
- 'tbprofiler': 'bactopia-tools/tbprofiler.md'
- 'Modules':
- 'abricate': 'bactopia-tools/abricate.md'
- 'abritamr': 'bactopia-tools/abritamr.md'
- 'agrvate': 'bactopia-tools/agrvate.md'
- 'amrfinderplus': 'bactopia-tools/amrfinderplus.md'
- 'blastn': 'bactopia-tools/blastn.md'
- 'blastp': 'bactopia-tools/blastp.md'
- 'blastx': 'bactopia-tools/blastx.md'
- 'bracken': 'bactopia-tools/bracken.md'
- 'btyper3': 'bactopia-tools/btyper3.md'
- 'busco': 'bactopia-tools/busco.md'
- 'checkm': 'bactopia-tools/checkm.md'
- 'clermontyping': 'bactopia-tools/clermontyping.md'
- 'defensefinder': 'bactopia-tools/defensefinder.md'
- 'ectyper': 'bactopia-tools/ectyper.md'
- 'emmtyper': 'bactopia-tools/emmtyper.md'
- 'fastani': 'bactopia-tools/fastani.md'
- 'gamma': 'bactopia-tools/gamma.md'
- 'genotyphi': 'bactopia-tools/genotyphi.md'
- 'hicap': 'bactopia-tools/hicap.md'
- 'hpsuissero': 'bactopia-tools/hpsuissero.md'
- 'ismapper': 'bactopia-tools/ismapper.md'
- 'kleborate': 'bactopia-tools/kleborate.md'
- 'kraken2': 'bactopia-tools/kraken2.md'
- 'legsta': 'bactopia-tools/legsta.md'
- 'lissero': 'bactopia-tools/lissero.md'
- 'mashdist': 'bactopia-tools/mashdist.md'
- 'mcroni': 'bactopia-tools/mcroni.md'
- 'meningotype': 'bactopia-tools/meningotype.md'
- 'midas': 'bactopia-tools/midas.md'
- 'mlst': 'bactopia-tools/mlst.md'
- 'mobsuite': 'bactopia-tools/mobsuite.md'
- 'mykrobe': 'bactopia-tools/mykrobe.md'
- 'ngmaster': 'bactopia-tools/ngmaster.md'
- 'pasty': 'bactopia-tools/pasty.md'
- 'pbptyper': 'bactopia-tools/pbptyper.md'
- 'phispy': 'bactopia-tools/phispy.md'
- 'plasmidfinder': 'bactopia-tools/plasmidfinder.md'
- 'pneumocat': 'bactopia-tools/pneumocat.md'
- 'quast': 'bactopia-tools/quast.md'
- 'rgi': 'bactopia-tools/rgi.md'
- 'sccmec': 'bactopia-tools/sccmec.md'
- 'seqsero2': 'bactopia-tools/seqsero2.md'
- 'seroba': 'bactopia-tools/seroba.md'
- 'shigapass': 'bactopia-tools/shigapass.md'
- 'shigatyper': 'bactopia-tools/shigatyper.md'
- 'shigeifinder': 'bactopia-tools/shigeifinder.md'
- 'sistr': 'bactopia-tools/sistr.md'
- 'spatyper': 'bactopia-tools/spatyper.md'
- 'ssuissero': 'bactopia-tools/ssuissero.md'
- 'staphopiasccmec': 'bactopia-tools/staphopiasccmec.md'
- 'stecfinder': 'bactopia-tools/stecfinder.md'
- 'tblastn': 'bactopia-tools/tblastn.md'
- 'tblastx': 'bactopia-tools/tblastx.md'
# - 'More Workflows':
# - 'Introduction': 'workflows/index.md'
# - 'Clean-Yer-Reads': 'workflows/clean-yer-reads.md'
# - 'Staphopia': 'workflows/staphopia.md'
# - 'Teton': 'workflows/teton.md'
# - 'Tutorials': 'tutorial.md'
- 'Impact & Outreach':
- 'Impact ': 'impact-and-outreach/index.md'
- 'Acknowledgements': 'impact-and-outreach/acknowledgements.md'
- 'Citations': 'impact-and-outreach/citations.md'
- 'Enhancements to OSS': 'impact-and-outreach/enhancements.md'
- 'Presentations': 'impact-and-outreach/presentations.md'
- Blog:
- blog/index.md