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_quarto.yml
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project:
type: website
# output directory used on gh-pages branch. format: YYMM
output-dir: "2503"
render:
- "!README.md"
- "!LICENSE"
- "!LICENSE.md"
- "!scripts"
- "!tmprepo"
- "!*.Rmd"
- "!*.md"
- "*.qmd"
website:
site-url: "https://nbisweden.github.io/workshop-ngsintro/"
favicon: "assets/favicon.png"
open-graph: true
image: "assets/images/seo.webp"
description: "A five day introductory workshop for beginners in the analysis of illumina short-read next-generation sequencing data which includes lectures and hands-on labs on a remote high-performance cluster. Topics covered include: working on the Linux command line, overview of sequence data formats and QC, DNA variant calling workflow and RNA sequence analyses workflow."
navbar:
logo: "assets/logos/nbis-scilifelab.png"
logo-alt: "logo"
right:
- text: "Home"
href: "index.html"
aria-label: "Home"
- text: "Schedule"
href: "home_schedule.html"
aria-label: "Schedule"
- text: "Contents"
href: "home_contents.html"
aria-label: "Contents"
- text: "Precourse"
href: "home_precourse.html"
aria-label: "Precourse"
- text: "Syllabus"
href: "home_syllabus.html"
aria-label: "Syllabus"
- text: "Info"
href: "home_info.html"
aria-label: "Info"
- icon: "github"
href: "https://github.com/NBISweden/workshop-ngsintro/"
aria-label: "GitHub"
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 >}}"
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.webp"
callout-icon: true
date: last-modified
date-format: "DD-MMM-YYYY"
lightbox: auto
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
hero: "/assets/images/slide-hero.webp"
title-slide-attributes:
data-background-image: "/assets/images/cover.webp"
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/2411/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/2411/home_schedule.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: true
filters:
- assets/custom.lua
- assets/fold-results.lua
- reveal-logo
# used site-wide
# project id on active cluster (dardel)
id_project: "edu25.uppmax"
# project id on fallback cluster (rackham)
id_project_backup: "naissXXXX-XX-XXXX"
# path to course working directory
path_workspace: "~/ngsintro"
# path to course resources on cluster
path_resources: "/sw/courses/ngsintro"
# url to active cluster (dardel)
url_cluster: "dardel.pdc.kth.se"
# url to backup cluster (rackham)
url_cluster_backup: "rackham.uppmax.uu.se"
# reservation ids
id_slurm_res_mon: "edu25-03-24"
id_slurm_res_tue: "edu25-03-25"
id_slurm_res_wed: "edu25-03-26"
id_slurm_res_thu: "edu25-03-27"
id_slurm_res_fri: "edu25-03-28"
# location is used to render the info page
# location options are linkoping, lund, umea, stockholm, uppsala or online
# one or more separated by commas or semicolon.
location: online
assistants:
- "AJ: Anna Johansson"
- "BV: Björn Viklund"
- "CK: Cormac Kinsella"
- "DA: Dag Ahren"
- "DE: Diana Ekman"
- "EB: Emre Balsever"
- "FB: Franziska Bonath"
- "FR: Fariba Roshanzamir"
- "GD: Guilherme Dias"
- "JD: Jyotirmoy Das"
- "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: "Breaks are planned for approximately 10:00 and 14:30 every day."
colors:
primary: "#95b540"
secondary: "#E9F2D1"