mkdocs.yml

site_name: SnakeNgs
site_description: Snakemake Pipeline for NGS data
site_author: Naoto Kubota
site_url: https://naotokubota/SnakeNgs
copyright: © 2024 Naoto Kubota
repo_url: https://github.com/NaotoKubota/SnakeNgs
repo_name: NaotoKubota/SnakeNgs

theme:
  name: material
  palette:
    # Palette toggle for automatic mode
    - media: "(prefers-color-scheme)"
      primary: amber
      accent: amber
      toggle:
        icon: material/brightness-auto
        name: Switch to light mode
    # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: amber
      accent: amber
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: amber
      accent: amber
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  font:
    text: Roboto
  language: en
  features:
    - search.suggest
    - search.highlight
    - navigation.instant
    - navigation.instant.progress
    - navigation.instant.prefetch
    - navigation.tracking
    - navigation.footer
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markdown_extensions:
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  - admonition
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extra:
  social:
    - type: "github"
      icon: fontawesome/brands/github
      link: "https://github.com/NaotoKubota"
    - type: "docker"
      icon: fontawesome/brands/docker
      link: "https://hub.docker.com/u/naotokubota"
    - type: "twitter"
      icon: fontawesome/brands/x-twitter
      link: "https://twitter.com/naoto_kubota"

edit_uri: edit/main/docs/

nav:
- Home: index.md
- Installation: installation.md
- Tutorial:
  - Fetching public NGS data: tutorial/Fetching.md
  - QC and mapping for RNA-seq: tutorial/RNAseq_preprocessing.md
  - UMI count from single-nucleus RNA-seq: tutorial/snRNAseq_count.md
  - QC, mapping, and peak calling for ChIP-seq/ATAC-seq: tutorial/ChIP-ATAC_preprocessing_callpeak.md
- Usage:
  - Fetching:
    - ngsFetch: usage/ngsFetch.md
  - RNA-seq:
    - preprocessing_RNAseq.smk: usage/preprocessing_RNAseq.md
    - preprocessing_RNAseq_single.smk: usage/preprocessing_RNAseq_single.md
    - rMATS.smk: usage/rMATS.md
    - SUPPA2_diffSplice.smk: usage/SUPPA2_diffSplice.md
    - Whippet.smk: usage/Whippet.md
    - MAJIQ.smk: usage/MAJIQ.md
    - LeafCutter.smk: usage/LeafCutter.md
  - snRNA-seq:
    - kb-nac.smk: usage/kb-nac.md
  - ChIP-seq:
    - preprocessing_ChIPseq.smk: usage/preprocessing_ChIPseq.md
    - preprocessing_ChIPseq_single.smk: usage/preprocessing_ChIPseq_single.md
    - callpeak_ChIPseq.smk: usage/callpeak_ChIPseq.md
  - ATAC-seq:
    - callpeak_ATACseq.smk: usage/callpeak_ATACseq.md
    - differential_ATACseq.smk: usage/differential_ATACseq.md
    - footprinting_ATACseq.smk: usage/footprinting_ATACseq.md
  - iCLIP-seq & HITSCLIP:
    - preprocessing_iCLIPseq.smk: usage/preprocessing_iCLIPseq.md
    - preprocessing_HITSCLIP.smk: usage/preprocessing_HITSCLIP.md
  - File format conversion:
    - bam2cram.smk: usage/bam2cram.md