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_quarto.yml
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project:
type: website
output-dir: _site
#date: today
#date-format: "YYYY"
website:
google-analytics: "G-9HW51GYWMM"
cookie-consent: true
title: "Cloud-SPAN Metagenomics"
favicon: images/cloud-span-icon.png
page-navigation: true # prev and next options at the bottom of each page
back-to-top-navigation: true
reader-mode: true
repo-url: https://github.com/Cloud-SPAN/nerc-metagenomics-v2q
repo-actions: [edit, issue]
page-footer:
left: |
Licensed under [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) 2021–24 by [Cloud-SPAN](https://cloud-span.york.ac.uk/)
# Licensed under [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) 2021–{{<meta date>}} by [Cloud-SPAN](https://cloud-span.york.ac.uk/)\
# Licensed under [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) 2018–{{<meta date>}} by the [Carpentries](https://carpentries.org/)\
# Licensed under [CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/) 2016–2018 by the [Data Carpentry](https://datacarpentry.org/)
# center:
# - text: "About"
# href: about.qmd
# - text: "FAQ"
# href: docs/faq/index.qmd
# - text: "License"
# href: license.qmd
# - text: "Trademark"
# href: trademark.qmd
right:
- icon: twitter
href: https://twitter.com/SpanCloud
aria-label: Quarto Twitter
- icon: github
href: https://github.com/Cloud-SPAN/nerc-metagenomics-v2q
aria-label: Quarto GitHub
# - icon: rss
# href: https://quarto.org/docs/blog/index.xml
# aria-label: Quarto Blog RSS
navbar:
background: lightblue
logo: images/cloud-span-icon.png
logo-alt: "Cloud-SPAN logo."
title: false
collapse-below: lg
left:
- text: Home
href: index.qmd
- text: Precourse Instructions
href: docs/miscellanea/precourse-instructions.qmd
- text: About
href: docs/miscellanea/about.qmd
# - text: License
# href: docs/miscellanea/license.qmd
# - text: Code of Conduct
# href: docs/miscellanea/codeofconduct.qmd
# - text: Help
# menu:
# - text: "Report a Bug"
# icon: "bug"
# href: "https://github.com/quarto-dev/quarto-cli/issues"
# - text: "Ask a Question"
# icon: "chat-right-text"
# href: "https://github.com/quarto-dev/quarto-cli/discussions"
# - text: "FAQ"
# icon: "question-circle"
# href: docs/faq/index.qmd
sidebar:
style: "docked"
collapse-level: 1
pinned: true
contents:
- section: Files and Directories
href: docs/lesson01-files-and-directories/index.qmd
contents:
- docs/lesson01-files-and-directories/01-understanding-file-systems.qmd
- docs/lesson01-files-and-directories/02-logging-onto-cloud.qmd
- docs/lesson01-files-and-directories/03-shell-introduction.qmd
- section: "Using the Command Line"
href: docs/lesson02-using-the-command-line/index.qmd
contents:
- docs/lesson02-using-the-command-line/01-navigating-file-directories.qmd
- docs/lesson02-using-the-command-line/02-working-with-file.qmd
- docs/lesson02-using-the-command-line/03-redirection.qmd
- section: "QC & Assembly"
href: docs/lesson03-qc-assembly/index.qmd
contents:
- docs/lesson03-qc-assembly/01-introduction-meta.qmd
- docs/lesson03-qc-assembly/02-QC-quality-raw-reads.qmd
- docs/lesson03-qc-assembly/03-assembly.qmd
- section: "Polishing"
href: docs/lesson04-polishing/index.qmd
contents:
- docs/lesson04-polishing/01-polishing-assembly.qmd
- docs/lesson04-polishing/02-QC-polished-assembly.qmd
- section: "Binning & Functional Annotation"
href: docs/lesson05-binning-functional-annotation/index.qmd
contents:
- docs/lesson05-binning-functional-annotation/01-binning.qmd
- docs/lesson05-binning-functional-annotation/02-binning_quality.qmd
- docs/lesson05-binning-functional-annotation/03-Functional-annotation.qmd
- section: "Taxonomic Annotations"
href: docs/lesson06-taxonomic-annotations/index.qmd
contents:
- docs/lesson06-taxonomic-annotations/01-taxonomic.qmd
- docs/lesson06-taxonomic-annotations/02-Diversity-tackled-with-R.qmd
- docs/lesson06-taxonomic-annotations/03-hands_on-diversity.qmd
# - section: "Automating Analyses with Bash Scripts"
# href: docs/lesson07-automation-bash-scripts/index.qmd
# contents:
# - docs/lesson07-automation-bash-scripts/01-scripting-intro.qmd
# - docs/lesson07-automation-bash-scripts/02-base-automation-script.qmd
# - docs/lesson07-automation-bash-scripts/03-adding-logging-and-control.qmd
# - docs/lesson07-automation-bash-scripts/04-creating-module-based-version.qmd
- section: "Extras"
contents:
- docs/miscellanea/extras/data.qmd
- docs/miscellanea/extras/glossary.qmd
- docs/miscellanea/extras/workflow.qmd
format:
html:
code-copy: true
# highlight-style: oblivion, haddock or monochrome # dracula # espresso #(nice greyish)
highlight-style: dracula
code-overflow: wrap
page-layout: full
theme: cosmo
css: styles.css
# theme:
# - styles.scss
toc: true
grid: # defaults
sidebar-width: 230px # 300px
body-width: 1040px # 900px
margin-width: 230px # 300px
gutter-width: 1.5rem # 1.5rem
lang: en
keywords: metagenomics, cloud computing, AWS, command line tools, data analysis, environmental science, learning resource
license: CC BY
doi: 10.5281/zenodo.12700160
appendix-style: none
title-block-style: none
execute:
freeze: auto
editor: visual