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_quarto.yml
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project:
type: book
output-dir: docs
execute-dir: project
book:
title: "Pathogen Genomics Course"
subtitle: "FA5 - Bioinformatics"
author:
- name: Pieter Moris
orcid: 0000-0003-4242-4939
url: https://pmoris.github.io
email: [email protected]
affiliations:
- Institute of Tropical Medicine Antwerp
- name: Wim Cuypers
orcid: 0000-0002-1895-3526
email: [email protected]
affiliations:
- University of Antwerp
- name: Pieter Monsieurs
orcid: 0000-0003-2214-6652
email: [email protected]
affiliations:
- Institute of Tropical Medicine Antwerp
- name: Oren Tzfadia
orcid: 0000-0002-7096-8063
email: [email protected]
affiliations:
- Institute of Tropical Medicine Antwerp
- name: Bethlehem Adnew
orcid: 0000-0002-6108-9534
email: [email protected]
affiliations:
- Armauer Hansen Research Institute
date: "2024-10-03"
date-format: long
# description: ...
# abstract: ...
# references: ...
# cover-image: cover.png
# downloads: [pdf,epub]
# copyright: "Copyright Pieter Moris, 2023. All Rights Reserved"
license: "CC BY 4.0"
chapters:
- index.qmd
# - content/intro.qmd
- part: "Introduction to the Unix shell"
chapters:
- content/unix/1-unix-intro.qmd
- content/unix/2-unix-setup.qmd
- content/unix/3-unix-enter-the-shell.qmd
- content/unix/4-unix-navigation.qmd
- content/unix/5-unix-files-and-dirs.qmd
- content/unix/6-unix-more-commands.qmd
- content/unix/7-unix-redirection.qmd
- content/unix/8-unix-variables-loops-scripts.qmd
- part: "Processing genomic data"
chapters:
- content/genomics/setup.qmd
- content/genomics/pipeline-overview.qmd
- content/genomics/tools-and-formats.qmd
- content/genomics/qc.qmd
- content/genomics/mapping.qmd
- content/genomics/variant-calling.qmd
- content/genomics/downloading_data.qmd
- content/genomics/phylogenetics.qmd
- content/genomics/results.qmd
# # - part: "Bioinformatics file formats and tools"
# # chapters:
# # - content/bioinf/bioinf-file-formats.qmd
# - part: "Malaria Molecular Surveillance"
# chapters:
# - content/mms/mms_usecases
# - content/mms/molecular_markers
# - content/mms/practical_variants_of_interest
# - content/mms/genetic_diversity
# - part: "Population genetics"
# chapters:
# - content/popgen/population_genetics
# - content/popgen/micro_evolution
# - content/popgen/practical_LD
# - content/popgen/visualisation
# - content/popgen/practical_PCA
# - content/popgen/relatedness
# - content/popgen/multilocus
# - content/popgen/ibd
# - content/popgen/population_structure
# - content/popgen/practical_ibd
# - part: "Case studies"
# - content/population-genetics.qmd
# - content/phylogenetics.qmd
# - part: "Computational literacy" # aka things that ~can~ will go wrong aka what I wish I had known
- content/references.qmd
# https://quarto.org/docs/books/book-structure.html#parts-appendices
# parts can either be a stand-alone file with intro
# or just a name for only grouping files below
appendices:
- content/unix/appendix-unix.qmd
# references: https://quarto.org/docs/books/book-structure.html#references
back-to-top-navigation: true
page-navigation: true
page-footer:
left: |
Unless otherwise noted, all content on this site is licensed under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/).
[{fig-alt="CC" height=30px}](https://creativecommons.org/licenses/by/4.0/) [{fig-alt="BY" height=30px}](https://creativecommons.org/licenses/by/4.0/)
<br>
© [Pieter Moris](https://pmoris.github.io) - [ITM Malariology](https://research.itg.be/en/organisations/malariology), 2024.
right: Built with [Quarto](https://quarto.org/).
# background: "#f8f9fa"
reader-mode: true
search:
location: sidebar
type: overlay
# https://quarto.org/docs/reference/projects/books.html#search
sidebar:
# https://quarto.org/docs/websites/website-navigation.html#side-navigation
style: "docked"
# style: "floating"
search: true
# background: dark
logo: content/assets/ITM-logo_col_rgb.png
logo-alt: Logo of Institute of Tropical Medicine Antwerp
logo-href: https://research.itg.be/en/organisations/malariology
# navbar:
# search: false
# https://quarto.org/docs/websites/website-navigation.html#hybrid-navigation
# page-footer:
# center:
# - text: "About"
# href: about.qmd
# - text: "License"
# href: license.qmd
# - text: "Trademark"
# href: trademark.qmd
favicon: content/assets/ITM-symbol_col_rgb.png
# twitter-card: true
# site-url: https://example.com
repo-url: https://cuypers-wim.github.io/FA5-bioinformatics/
# repo-actions: [source]
# sharing: [twitter, facebook]
# comments:
# hypothesis: true
toc: true
toc-depth: 4
toc-expand: true
# toc-location: left
number-sections: true
# number-depth: 2
# citation-location: margin
reference-location: margin
bibliography: content/references.bib
appendix-style: default
format:
html:
theme:
light: [flatly, ./styles/custom.scss]
# dark: [darkly, ./styles/custom.scss]
# https://quarto.org/docs/websites/website-tools.html#dark-mode
# If a navbar has been specified, the toggle will appear in the top right corner of the nav bar.
# If there is no navbar present, but a sidebar has been specified, the toggle will appear in the same location that the sidebar tools appears (adjacent to the title or logo in the sidebar).
# If there is no navbar or sidebar present, the toggle will appear in the top right corner of the page.
highlight-style: arrow # monokai nord dracula arrow
mainfont: 'Source Sans 3'
# mainfont: 'Source Sans Variable'
# mainfont: \"Source Sans 3 VF\"
# mainfont: 'Mulish'
# mainfont: 'Lato'
monofont: 'Fira Code'
linestretch: 1.5
code-fold: true
html-math-method: katex
lightbox: true
# PrettyPDF-pdf:
# documentclass: scrreprt
# keep-tex: true
# include-in-header:
# text: |
# \usepackage{fvextra}
# \DefineVerbatimEnvironment{Highlighting}{Verbatim}{breaklines,commandchars=\\\{\}}
# include-before-body:
# text: |
# \RecustomVerbatimEnvironment{verbatim}{Verbatim}{
# showspaces = false,
# showtabs = false,
# breaksymbolleft={},
# breaklines
# }
# pdf:
# # documentclass: scrreprt
# documentclass: scrbook
# keep-tex: true
# include-in-header:
# text: |
# \usepackage{fvextra}
# \DefineVerbatimEnvironment{Highlighting}{Verbatim}{breaklines,commandchars=\\\{\}}
# include-before-body:
# text: |
# \RecustomVerbatimEnvironment{verbatim}{Verbatim}{
# showspaces = false,
# showtabs = false,
# breaksymbolleft={},
# breaklines
# }
# epub:
# toc: true
strip-comments: true
editor: source