mkdocs.yml

# mkdocs w/ material theme

site_name: 'McGill SI 2018 GenEpi'
site_description: 'McGill Summer Institue - Genomic Epidemiology of Infectious Diseaes'
site_author: 'Anna Syme, Torsten Seemann'
site_url: 'https://sepsis-omics.github.io/mcgill-si-2018'

# Will add github and edit links for each page
#repo_name: 'sepsis-omics/mcgill-si-2018'
#repo_url: 'https://github.com/sepsis-omics/mcgill-si-2018'

# Copyright
copyright: '© Melbourne Bioinformatics, The University of Melbourne, Australia.'

# https://squidfunk.github.io/mkdocs-material/getting-started/
theme:
  name: 'material'
  language: 'en'
  palette:
    primary: 'teal'
    accent: 'teal'
  logo:
    icon: 'blur_on'
  feature:
    tabs: true

# Customization
extra:
  social:
    - type: 'dropbox'
      link: 'http://bit.ly/GenomicEpi18'
    - type: 'github'
      link: 'https://github.com/sepsis-omics/mcgill-si-2018'
    - type: 'bug'
      link: 'https://github.com/sepsis-omics/mcgill-si-2018/issues'
    - type: 'twitter'
      link: 'https://twitter.com/MelBioInf'
    - type: 'internet-explorer'
      link: 'https://www.melbournebioinformatics.org.au/'

markdown_extensions:
  - admonition
  - smarty
  - tables
  - markdown_include.include
  - codehilite

extra_css:
    - css/sepsis.css

pages:
  - Home: index.md

  - Day 1:
    - Agenda: day1.md
    - Intro to Galaxy: modules/galaxy-intro-1/index.md
    - Training data set: modules/data-dna/index.md
    - Quality control: modules/fastqc/index.md
    - Genome assembly: modules/spades/index.md
    #- Genome annotation: modules/prokka/index.md
    #- Using Galaxy: modules/galaxy/index.md
    #- Starting with Galaxy: modules/galaxy/index.md

  - Day 2:
    - Agenda: day2.md
    - Detecting contamination: modules/kraken/index.md
    - Variant finding: modules/snippy/index.md
    - Genome annotation: modules/prokka/index.md
    - Build a tree: modules/build_a_tree/index.md
    #- Read trimming: modules/trimmomatic/index.md
    #- Genome assembly with Velvet: modules/velvet/index.md
    #- Public data → assembly, annotation: modules/access_data/index.md

  - Day 3:
    - Agenda: day3.md
    - Transmission practical: modules/transmission/index.md

  - Day 4:
    - Agenda: day4.md
    - Predicting antimicrobial resistance: modules/abricate/index.md
    - Nanopore viral genomics: modules/nanopore-ebola/index.md

  - Day 5:
    - Agenda: day5.md

  - Journal Club:
    - Papers: journal_club.md

  - Extras:
    - Agenda: extras.md
    - Skills practice: modules/extra/index.md
    - Viewing genomes with Artemis: modules/artemis/index.md
    - Galaxy workflows: modules/workflows/index.md
    - Viral genome sequencing: modules/viral_genomes/index.md
    - Read trimming: modules/trimmomatic/index.md

  - About:
    - Acknowledgements: about/index.md

  #- Proteomics:
  #    - Protein Identification: modules/xtandem/index.md
  #    - Pathway annotation and prediction: modules/pathway_tools/annotation/index.md

  #- Metabolomics:
  #    - Metabolite identification: modules/xcms/index.md
      #- Draft: modules/xcms/metab_draft.md

  #- Command-Line:
  #  - PacBio assembly with command line tools: modules/cmdline_assembly/index.md
  #  - Spades assembly - commandline: modules/spades_cmdline/index.md
  #  #- Genome annotation - commandline:

  #- Txomics:
  #  - Overview: modules/transcriptomics.md
  #  - Dataset: modules/data-rna/index.md
  #  - Transcriptome assembly: modules/stringtie/index.md
  #    - Differential gene expression using Galaxy and Degust: modules/dge/index.md
  #    - Differential gene expression using Kallisto and Degust: modules/kallisto/index.md
       #- Salmon: modules/salmon/index.md

  #- Bonus:
  #  - Additional material - skills practice: modules/extra/index.md

    #- Metagenomics with FROGS: modules/frogs/index.md
    #- PacBio assembly with SMRT portal: modules/pacbio/index.md
    #- Annotation using command line tools: modules/cmdline_prokka/index.md
    #- Bash scripts: modules/scripts/index.md
    #- Genomics workshop overview: modules/workshop_overview/index.md

# DONT WORK:

#    - Investigate a TB outbreak: modules/transmission/index.md
    #- JBrowse: modules/jbrowse/index.md
    #- Differential Gene Expression: intro/dge/index.md
    #- Pan genome: intro/roary/index.md