_quarto.yml

project:
  type: book
  output-dir: docs
  execute-dir: project

book:
  title: "Introduction to Bioinformatics for Malaria Molecular Surveillance"
  subtitle: "International Training Progamme - Fighting Malaria Across Borders - Bioinformatics Module"

  author:
    - name: Pieter Moris
      orcid: 0000-0003-4242-4939
      url: https://pmoris.github.io
      email: pmoris@itg.be
      affiliations:
        - name: Institute of Tropical Medicine Antwerp
          url: https://www.itg.be
  date: "2024-05-02"
  date-format: long

  # description: ...
  # abstract: ...
  # references: ...
  # cover-image: cover.png
  # downloads: [pdf,epub]

  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: "Introduction to R"
      chapters:
        - content/r/r-intro.qmd
        - content/r/r-resources.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
    #   - 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: |
      © [Pieter Moris](https://pmoris.github.io) - [Institute of Tropical Medicine Antwerp - Malariology Unit](https://research.itg.be/en/organisations/malariology), 2024.
    center: |
      Unless otherwise noted, all content on this site is licensed under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/).
      [![](https://mirrors.creativecommons.org/presskit/icons/cc.svg){fig-alt="CC" height=1.2em}](https://creativecommons.org/licenses/by/4.0/) [![](https://mirrors.creativecommons.org/presskit/icons/by.svg){fig-alt="BY" height=1.2em}](https://creativecommons.org/licenses/by/4.0/)
    right: Built with [Quarto](https://quarto.org/).
    # background: "#f8f9fa"

  reader-mode: true

  search:
    location: sidebar
    type: textbox # overlay
    show-item-context: true
    # 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 # make logo return to the root of the page

  # 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://pmoris.github.io/FiMAB-bioinformatics/
  repo-url: https://github.com/pmoris/FiMAB-bioinformatics
  repo-actions: [source, issue]
  # 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: "Atkinson Hyperlegible Next"
    # mainfont: "Source Sans 3"
    # mainfont: 'Mulish'
    # mainfont: 'Lato'
    monofont: "Fira Code"
    linestretch: 1.5
    code-fold: true
    html-math-method: katex
    lightbox: true
    # page-layout: full
  # 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