_quarto.yml

project:
  type: website

website:
  title: "HPC Lab" 
  navbar:
    logo: /img/logo.png
    background: primary
    left:
      - text: "Home"
        file: index.qmd
      - text: "HPC Launch"
        file: develop/hpc-intro.qmd 
      - text: "HPC Pipes"
        file: develop/p0-intro.qmd
      - text: "Workshop"
        file: workshop/pipes-requirements.qmd 
    right: 
      - icon: github
        href: https://github.com/hds-sandbox
        aria-label: GitHub
      - icon: linkedin
        href: https://www.linkedin.com/company/ucph-heads/
        aria-label: LinkedIn
 
  sidebar:
    - title: "HPC Pipes"
      style: "docked"
      search: true
      contents:
        - develop/p0-intro.qmd
        - section: "Computational environments"
          contents:
            - develop/e1-fair_envs.qmd
            - develop/e2-docker.qmd
            - develop/e3-singularity.qmd
            - develop/e4-RDM_containers.qmd
            - develop/cheat_sheet.qmd
        - section: "Pipeline languages"
          contents:
            - develop/p1-fair_workflow.qmd 
            - develop/p2-smk.qmd
            - develop/p3-nextflow.qmd
            - develop/p4-workflow_envs.qmd
            - develop/exercise_pipes.qmd
    - title: "HPC Launch"
      style: "docked"
      search: true
      contents:
        - section: "HPC systems"
          contents: 
            - develop/hpc-intro.qmd 
            - develop/hpc-jobs.qmd
            - develop/hpc-programming.qmd
        - section: "Data management"
          contents: 
            - develop/hpc-data_transfer.qmd
            - develop/hpc-ssh_keys.qmd
        - section: "Quizzes"
          contents:
            - develop/exercise_launch.qmd
    - title: "Workshop"
      style: "docked"
      search: true
      contents:
        - section: "HPC Pipes"
          contents: 
            - workshop/pipes-requirements.qmd
            - section: "Day 1"
              contents: 
                - workshop/pipes-ex-envs.qmd
                - workshop/pipes-ex-smk.qmd
            - section: "Day 2"
              contents: 
                - text: "Day 2 - Part 3"            
                  href: workshop/pipes-ex-smk-self.qmd
                - text: "Day 2 - Part 4"
                  href: workshop/pipes-ex-smk-fast.qmd
        - section: "HPC Launch"
          contents: 
            - workshop/launch-requirements.qmd
            - workshop/cookiecutter.qmd
        - text: "UCloud setup"
          href: workshop/UCloud.qmd


copyright: CC-BY-SA 4.0 license

format:
  html:
    theme: 
      light: [materia, css/materialight.scss]
      dark: darkly
    toc: true
    code-fold: true
    css: include/webex.css
    include-after-body: include/webex.js
filters:
  - css/custom-callout.lua