knowledge/mkdocs.yml at main · Juke34/knowledge · GitHub

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# Project information
site_name: 'Jacques Dainat Bioinformatics Knowledge'
site_author: 'Jacques Dainat'
site_url: 'https://juke34.github.io/knowledge/'
site_description: Some bioinformatics knowledge gathered by Jacques Dainat
site_dir: public # When you build your site, all of the files are written to the directory assigned to the site_dir configuration option (defaults to "site")

# Repository
repo_name: 'knowledge'
repo_url: 'https://github.com/juke34/knowledge'
edit_uri: edit/main/docs/ # Allow to replace edit/master/docs use by default

# Configuration
theme:
  name: material
  #logo: pages/img/ # logo top left page
  search_index_only: true
  include_search_page: true
  features:
    - announce.dismiss
    - content.action.edit
    - content.action.view
    - content.code.annotate
    - content.code.copy
  # - content.tabs.link
    - content.tooltips
    - header.autohide
    # - navigation.expand
    - navigation.footer
    - navigation.indexes
    # - navigation.instant
    # - navigation.prune
    # - navigation.sections # collapse subsections
    - navigation.tabs
    # - navigation.tabs.sticky
    - navigation.top
    - navigation.tracking
    - search.highlight
    - search.share
    - search.suggest
    - toc.follow
    - toc.integrate # remove table of content on the right side
  palette:
    - scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode

# Extensions
markdown_extensions:
  - admonition
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.tabbed
  - pymdownx.snippets:
      base_path: docs
  - attr_list
  - tables
  - toc:
    #  toc_depth: 3
      permalink: '#'

# Plugins
plugins:
  - search:
      separator: '[\s\-,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])'
  - minify:
      minify_html: true
  #- external-markdown
  - macros
  - include-markdown

# css
extra_css:
  - stylesheets/extra.css

# javascripts
extra_javascript:
  - https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js
  - javascripts/tablesort.js

# Customization
extra:
#  homepage:  # Page displayed when clicking the logo
  history_buttons: false
  # --- set whole scope variables ---
  color_table_header: "#333a99"

# page tree
nav:
    - Home: README.md
    - Bioinformatics:
      - Formats :
        - Specification :
          - BAM / SAM : bioinformatics/format/specification/bam_and_sam.md
          - BED v1 : bioinformatics/format/specification/bed.md
          - CIGAR : bioinformatics/format/specification/cigar.md
          - CRAM v3.1 : bioinformatics/format/specification/cram.md
          - GFF / GTF all versions : bioinformatics/format/specification/gxf.md
          - Markdown : bioinformatics/format/specification/markdown.md
          - SUGAR : bioinformatics/format/specification/sugar.md
          - TEXTILE (Wiki) : bioinformatics/format/specification/textile.md
          - VCF v4.4 : bioinformatics/format/specification/vcf.md
          - VULGAR : bioinformatics/format/specification/vulgar.md
          - Interesting ressources about formats: bioinformatics/format/specification/interesting_ressources.md
        - Conversion :
          - GFF to :
            - GTF: bioinformatics/format/conversion/gff_to_gtf.md
            - BED: bioinformatics/format/conversion/gff_to_bed.md
        - Handling :
          - FASTA : bioinformatics/format/handling/split_fasta.md
      - Annotation :
        - Genome : bioinformatics/annotation/structural/annotation_tools_genome.md
        - Mitochondrion : bioinformatics/annotation/structural/annotation_tools_mitome.md
        - Chloroplast : bioinformatics/annotation/structural/annotation_tools_plastome.md
        - Plasmid : bioinformatics/annotation/structural/annotation_tools_plasmidome.md
      - Classification : bioinformatics/taxonomic_classification.md
      - Variant annotation : bioinformatics/variant_annotation.md
      - Visualisation : bioinformatics/data_visualisation.md
    - Cluster :
      - Schedulers commands comparison : cluster/scheduler_rosetta.md
      - Slurm : cluster/slurm.md
      - Rackham : cluster/rackham.md
      - Screen : cluster/screen.md
    - Programming :
        - Bash :
          - Lecture : programming/bash/bash_lecture.md
          - Cheat sheet : programming/bash/bash_cheat_sheet.md
          - Useful commands : programming/bash/bash_other.md
        - Bioconda : programming/bioconda/bioconda.md
        - Git : programming/git/git.md
        - Perl :
          - Perl code profiler : programming/perl/perl_code_profiler.md
        - Python : programming/python/python.md
        - R : programming/r/r.md
        - Nextflow : programming/nextflow/nextflow.md
    - Resource:
      - Course : resource/course.md
      - Sites :  resource/sites.md
      - Blogs : resource/blogs.md
    - Sequencing : sequencing/sequencing.md
    - Statistics : statistics/statistics.md