_quarto.yml

project:
  type: website
  # output directory used on gh-pages branch. format: YYMM
  output-dir: "2411"
  render: 
    - "!README.md"
    - "!LICENSE"
    - "!LICENSE.md"
    - "!scripts"
    - "!tmprepo"
    - "!*.Rmd"
    - "!*.md"
    - "*.qmd"

website:
  image: "assets/images/featured.jpg"
  favicon: "assets/favicon.png"
  navbar:
    logo: "assets/logos/nbis-scilifelab.png"
    logo-alt: "logo"
    right:
      - text: "Home"
        href: "index.html"
      - text: "Schedule"
        href: "home_schedule.html"
      - text: "Contents"
        href: "home_contents.html"
      - text: "Precourse"
        href: "home_precourse.html"
      - text: "Syllabus"
        href: "home_syllabus.html"
      - text: "Info"
        href: "home_info.html"
  page-footer:
    border: false
    left: "{{< meta current_year >}} [NBIS](https://nbis.se) | [GPL-3 License](https://choosealicense.com/licenses/gpl-3.0/)"
    right: "Published with [Quarto](https://quarto.org/) v{{< meta quarto_version >}}"
  site-url: "https://nbisweden.github.io/workshop-ngsintro/"

format:
  html:
    quarto-required: ">=1.4.0"
    include-in-header: "assets/include_head.html"
    theme: "assets/css/styles.scss"
    smooth-scroll: true
    toc: true
    toc-depth: 4
    toc-location: right
    number-sections: true
    number-depth: 4
    code-fold: false
    code-tools: false
    code-copy: true
    code-overflow: wrap
    df-print: paged
    standalone: false
    fig-align: left
    title-block-banner: "assets/images/banner.jpg"
    callout-icon: true
    date:  last-modified
    date-format: "DD-MMM-YYYY"
    image: "assets/images/featured.png"
  revealjs:
    quarto-required: ">=1.4.0"
    include-in-header: "assets/include_head.html"
    theme: ["default","assets/css/slides.scss"]
    df-print: paged
    width: 1280
    height: 720
    transition: "fade"
    transition-speed: "fast"
    smaller: false
    incremental: false
    scrollable: false
    slide-level: 2
    slide-number: true
    progress: true
    date:  last-modified
    date-format: "DD-MMM-YYYY"
    fig-align: left
    chalkboard: true
    callout-icon: true
    image: "/assets/images/featured.jpg"
    hero: "/assets/images/slide-hero.png"
    title-slide-attributes:
      data-background-image: "/assets/images/cover.jpg"
      data-background-size: "cover"
      data-background-opacity: "1"
    header-logo-left: /assets/logos/nbis.png
    header-logo-left-height: 25px
    header-logo-left-url: https://nbisweden.github.io/workshop-ngsintro/home_contents.html
    header-logo-right: /assets/logos/scilifelab.png
    header-logo-right-height: 25px
    header-logo-right-url: https://nbisweden.github.io/workshop-ngsintro/home_contents.html
    template-partials:
      - "assets/title-slide.html"
      
bibliography: references.bib
csl: apa.csl

knitr:
  opts_chunk:
    results: hold

execute:
  eval: true
  echo: true
  warning: false
  message: false
  freeze: false

filters:
  - assets/custom.lua
  - reveal-logo

# used site-wide wherever uppmax project ids are used
uppmax_project: naiss2024-22-1375
nsc_project: naiss2024-22-1375

# location options are linkoping, lund, umea, uppsala or online. For rendering the info page.
# one or more separated by commas or semicolon. online doesn't display any location info.
location: linkoping
assistants:
 - "AJ: Anna Johansson"
 - "BV: Björn Viklund"
 - "CK: Cormac Kinsella"
 - "DA: Dag Ahren"
 - "EB: Emre Balsever"
 - "FB: Franziska Bonath"
 - "FR: Fariba Roshanzamir"
 - "GD: Guilherme Dias"
 - "JH: Jason Hill"
 - "JB: Joakim Bygdell"
 - "JT: Jeanette Tångrot"
 - "KL: Katarina Lejonlid"
 - "KB: Kristina Benevides"
 - "LK: Linda Köhn"
 - "LS: Lucile Soler"
 - "LV: Louella Vasquez"
 - "MD: Martin Dahlö"
 - "MG: Maxime Garcia"
 - "ML: Malin Larsson"
 - "MM: Markus Mayrhofer"
 - "MP: Martin Pippel"
 - "MR: Miguel Redondo"
 - "MV: Massimiliano Volpe"
 - "NN: Nina Norgren"
 - "OP: Olga Vinnere Pettersson"
 - "PA: Prasoon Agarwal"
 - "PP: Paul Pyl"
 - "RF: Roy Francis"
 - "SD: Sebastian DiLorenzo"
 - "VK: Varsith Konda"
 - "YL: Yuan Li"
schedule_message: "Coffee breaks are planned for approximately 10:00 and 14:30 every day."
colors:
  primary: "#95b540"
  secondary: "#E9F2D1"

# r packages needed for the workshop
# used in home_precourse.Rmd
# split into cran and bioc packages
# if a package is needed by students and repo, add to _student
# if a package is only needed for repo (build, rendering etc), add to _repo
# NOT USED FOR GITHUB ACTIONS
packages:
  packages_cran_student:
   - BiocManager
   - remotes
   - dplyr
   - ggplot2
   - pheatmap
   - stringr
   - tidyr
  packages_bioc_student:
   - DESeq2
   - edgeR
   - goseq
   - GO.db
   - org.Mm.eg.db
   - reactome.db
  packages_github_student:
  packages_cran_repo:
   - here
   - htmlTable
   - knitr
   - leaflet
   - lubridate
   - readxl
   - writexl
   - yaml
  packages_bioc_repo:
  packages_github_repo: