mkdocs.yml

site_name: PoolSeqFlow
site_url: https://ozankiratli.github.io/PoolSeqFlow/
site_author: Ozan L. Z. Kiratli
site_description: >-
  A Nextflow pipeline for allele frequency analysis from pooled Illumina
  sequencing data.

repo_url: https://github.com/ozankiratli/PoolSeqFlow
repo_name: ozankiratli/PoolSeqFlow
# Every page is generated from the manual, so the edit link points at the manual
# rather than at the page's own source, which nobody should edit.
edit_uri_template: edit/main/manual/PoolSeqFlow-manual.md

copyright: >-
  Apache 2.0 · Ozan L. Z. Kiratli

docs_dir: docs
site_dir: site

theme:
  name: material
  language: en
  logo: assets/logo.svg
  favicon: assets/favicon.svg

  # Dark first: the entry listed first is the default, so a visitor with no
  # stored preference lands on slate. The toggle switches to the light scheme.
  palette:
    - scheme: slate
      primary: custom
      accent: custom
      toggle:
        icon: material/weather-night
        name: Switch to light mode
    - scheme: default
      primary: custom
      accent: custom
      toggle:
        icon: material/weather-sunny
        name: Switch to dark mode

  font:
    text: Source Sans 3
    code: JetBrains Mono

  features:
    # No navigation.sections: with it every section is a permanently open group, so the
    # whole manual sits in the sidebar at once. Collapsed, a section opens when it is the
    # one being read and stays shut otherwise.
    - navigation.indexes       # a section can have its own landing page
    - navigation.tracking      # URL follows the anchor being read
    - navigation.top
    - navigation.footer
    - toc.follow
    - search.suggest
    - search.highlight
    - search.share
    - content.code.copy
    - content.action.edit
    - content.tooltips

  icon:
    repo: fontawesome/brands/github
    edit: material/pencil

extra_css:
  - stylesheets/extra.css

extra_javascript:
  - javascripts/header-link.js
  - javascripts/mathjax.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/ozankiratli/PoolSeqFlow
      name: PoolSeqFlow on GitHub
    - icon: fontawesome/solid/globe
      link: https://ozankiratli.github.io
      name: ozankiratli.github.io
  generator: false

markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - def_list
  - footnotes
  - md_in_html
  - tables
  - toc:
      permalink: true
      permalink_title: Link to this section
      toc_depth: 3
  - pymdownx.arithmatex:
      generic: true
  - pymdownx.betterem
  - pymdownx.caret
  - pymdownx.details
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.smartsymbols
  - pymdownx.snippets:
      base_path:
        - .
        - docs
      check_paths: true
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - pymdownx.tilde

plugins:
  - search

# A link to a heading that no longer exists is a build failure, not a dead
# anchor on the published site. dev/scripts/build_docs.py already refuses to
# emit one; this catches the same mistake in CHANGELOG.md, which is included
# verbatim and does not pass through it.
validation:
  links:
    anchors: warn

# Everything below this line is generated by dev/scripts/build_docs.py from
# manual/PoolSeqFlow-manual.md. Edits here are overwritten.
nav:
  - Home: index.md
  - Getting Started:
      - getting-started/index.md
      - Install: getting-started/install.md
      - Quick Start: getting-started/quick-start.md
      - Upgrading: getting-started/upgrading.md
  - Concepts:
      - concepts/index.md
      - Scientific Rationale: concepts/scientific-rationale.md
      - Design Decisions: concepts/design-decisions.md
      - The Filter Chain: concepts/filter-chain.md
      - Interpreting Results: concepts/interpreting-results.md
  - Pipeline:
      - pipeline/index.md
      - Steps: pipeline/steps.md
      - Resume Logic: pipeline/resume.md
      - Directory Layout: pipeline/directories.md
  - Configuration:
      - configuration/index.md
      - Metadata: configuration/metadata.md
      - Multi-run: configuration/multi-run.md
      - Resources: configuration/resources.md
      - Trimming & Clipping: configuration/trimming.md
      - Alignment & Cleaning: configuration/filters.md
      - Variant Calling: configuration/variant-calling.md
      - Filtering & Frequency Calculations: configuration/filtering.md
      - Annotations: configuration/annotations.md
  - Analysis:
      - analysis/index.md
      - Configuration: analysis/configuration.md
      - Verification: analysis/verification.md
      - Output: analysis/output.md
  - Modules:
      - modules/index.md
      - In common: modules/common.md
      - basicstats: modules/basicstats.md
      - association: modules/association.md
      - mds: modules/mds.md
  - Development:
      - development/index.md
      - History: development/history.md
      - Rationale: development/principles.md
      - Verification: development/verification.md
      - Claude Code: development/claude-code.md
  - Reference:
      - Troubleshooting: reference/troubleshooting.md
      - Bibliography: reference/bibliography.md
      - Changelog: reference/changelog.md
      - Citation & License: reference/citation.md