mkdocs.yml

site_name: ABRPI-Training
site_description: Tutorials for analysing bacterial omics data
site_author: Anna Syme, Torsten Seemann
site_favicon: favicon.ico

site_url: 'http://sepsis-omics.github.io/tutorials/'

repo_name: 'sepsis-omics/tutorials'
repo_url: 'https://github.com/sepsis-omics/tutorials'

copyright: '© The authors; 2016-'

#theme: yeti
theme: material
extra:
    feature:
        tabs: true
    social:
        - type: 'coffee'
          link: 'https://omics.data.edu.au/'
        - type: 'github'
          link: 'https://github.com/sepsis-omics/tutorials'
        - type: 'bug'
          link: 'https://github.com/sepsis-omics/tutorials/issues'


markdown_extensions:
    - admonition
    - smarty
    - tables
    - markdown_include.include
    - codehilite
    - pymdownx.details
    - footnotes
extra_css:
    - css/sepsis.css

pages:
- Home: index.md
- Genomics:
    - Genomics workshop overview: modules/workshop_overview/index.md
    #- Using Galaxy: modules/galaxy/index.md
    - Starting with Galaxy: modules/galaxy/index.md
    - Training dataset: modules/data-dna/index.md
    - Quality control: modules/fastqc/index.md
    - Merge reads with Pear: modules/pear/index.md
    # - Read trimming: modules/trimmomatic/index.md
    # - Workflow - merge and trim: modules/workflow-pear-trim/index.md
    - Genome assembly with Velvet: modules/velvet/index.md
    - Genome assembly with Spades: modules/spades/index.md
    - Genome annotation: modules/prokka/index.md
    - Variant finding: modules/snippy/index.md
    # Snippy core
    # Gubbins
    - Public data → assembly, annotation: modules/access_data/index.md
    - Finding antibiotic-resistant genes: modules/abricate/index.md
    - Viral genome sequencing: modules/viral_genomes/index.md
    - Galaxy workflows: modules/workflows/index.md
    - Metagenomics with FROGS: modules/frogs/index.md
    - Sample identification with Kraken: modules/kraken/index.md
    - PacBio assembly with SMRT portal: modules/pacbio/index.md
    - PacBio assembly with command line tools: modules/cmdline_assembly/index.md
    - Spades assembly - commandline: modules/spades_cmdline/index.md
    - Genome alignment with Mauve: modules/mauve/index.md
    - Pangenomes with Roary/Phandango - command line: modules/roary/index.md
    - Pangenomes with Roary/Phandango - Galaxy: modules/roary-galaxy/index.md
    #- Annotation using command line tools: modules/cmdline_prokka/index.md
    #- Bash scripts: modules/scripts/index.md

- Transcriptomics:
#  - Overview: modules/transcriptomics.md
#  - Dataset: modules/data-rna/index.md
#  #- Quality control: modules/fastqc/index.md
#  #- Read trimming: modules/trimmomatic/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
#- Advanced:
    #- Differential Gene Expression: intro/dge/index.md
    #- Pan genome: intro/roary/index.md
    #- Artemis: modules/artemis/index.md
    #- JBrowse: modules/jbrowse/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

- About: about/index.md