_quarto.yml

project:
  type: book
  output-dir: docs

book:
  title: "Fundamentals of computational biology"
  subtitle: "Lecture notes"
  author: 
    - name: "Camilo García-Botero"
      orcid: 0000-0002-0426-7007
      url: https://camilogarciabotero.github.io/
      # affiliation: Universidad EAFIT
  cover-image: figs/cover-03.png
  # search: true  

  # citation:
  #   type: book
  #   # container-title: "Journal of Data Science Software"
  #   doi: 10.5281/zenodo.6468280
  #   url: https://camilogarciabotero.github.io/biocomp-book/

  date: today
  date-format: "YYYY-MM-DD"

  repo-url: https://github.com/camilogarciabotero/biocomp-book
  site-url: https://camilogarciabotero.github.io/biocomp-book/
  repo-actions: [edit, issue]
  repo-branch: main
  # downloads: [pdf]
  google-analytics: "G-QFWWJGZHLD"
  # sharing: [twitter]
  sidebar:
    style: floating

  page-footer: 
    border: true
    center: "Made with [Quarto](https://quarto.org/). Under [GNU GPL 3.0](https://github.com/camilogarciabotero/biocomp-book/blob/main/LICENSE). Buy me coffee [{{< fa mug-saucer >}}](https://www.paypal.com/paypalme/camilogarciabotero) and visit me at [{{< fa house >}}](https://camilogarciabotero.github.io/)"

  chapters:
    - index.qmd
    - intro.qmd
    - part: "The command line"
      chapters:
        - chs-command-line/welcome-to-command-line.qmd
        - chs-command-line/git-and-github.qmd
        - chs-command-line/package-managers.qmd
        - chs-command-line/hpc-notions.qmd
    - part: "Intro. to algorithms"
      chapters:
        - chs-intro-algorithms/algorithm-thinking.qmd
        - chs-intro-algorithms/algorithm-techniques.qmd
        - chs-intro-algorithms/data-structures.qmd
    - part: "Sequence analysis"
      chapters:
        - chs-sequence-analysis/introduction-to-sequence-analysis.qmd
        - chs-sequence-analysis/sanger-analysis.qmd
        - chs-sequence-analysis/sequence-alignments.qmd
        - chs-sequence-analysis/NGS-TGS-principles.qmd
    - part: "Phylogenetics"
      chapters:
        - chs-phylogenetics/phylogenetic-reconstructions.qmd
        - chs-phylogenetics/phylogenomics.qmd
    - part: "Genomics"
      chapters:
        - chs-genomics/genome-assembly.qmd
        - chs-genomics/genome-annotation.qmd
        - chs-genomics/variant-calling-analysis.qmd
        - chs-genomics/comparative-genomics.qmd
    - part: "Metagenomics"
      chapters:  
        - chs-metagenomics/metagenomic-sequencing.qmd
        # - chs-metagenomics/comparative-metagenomics.qmd
    - part: "Structural bioinformatics"
      chapters:
        - chs-bio-structural/intro-structural-bioinfo.qmd
        - chs-bio-structural/molecular-docking.qmd
    - part: "Challenges"
      chapters:
        - chs-challenges-demos/unix-challenges.qmd
        - chs-challenges-demos/seq-analysis-challenges.qmd
        - chs-challenges-demos/genome-analysis-challenges.qmd
    #     - chs-challenges-demos/demo-sanger-processing.qmd
    #     - chs-challenges-demos/demo-sequence-alignment.qmd
    #     - chs-challenges-demos/demo-phylogenetics.qmd
    #     - chs-challenges-demos/demo-reads-assessment.qmd
    #     - chs-challenges-demos/demo-genome-assembly.qmd
    - part: Appendix
      chapters: 
        - HISTORY.qmd 
    - references.qmd

bibliography: references.bib
reference-location: margin
crossref: 
  lst-title: Code

comments:
  hypothesis: true
  giscus: 
      repo: camilogarciabotero/biocomp-book
      theme: transparent_dark

execute:
  cache: true

google-scholar: true

format:
  html:
    theme: 
      light: 
      - flatly
      - style/fonts.scss
      dark: 
      - darkly
      - style/fonts.scss
    code-link: true
    code-copy: hover
    df-print: paged
    fig-align: center
    mainfont: Atkinson Hyperlegible
    monofont: JetBrains
    highlight-style: ayu
    # mainfont: sora Fira Code nord github oblivion arrow
  # pdf:
  #   documentclass: book
  #   code-block-border-left: false
  #   toc-depth: 2
  #   lof: true
  #   lot: true
  #   title-bg-image: figs/cover.png
  # pdf:
  #   documentclass: scrreprt