_pkgdown.yml

development:
  mode: devel
template:
  package: preferably
  bootstrap: 5
  params:
    ganalytics: "281550496"
    toggle: manual
    docsearch:
      api_key: "937cedcd467c204b19fc155c5f35019b"
      index_name: "scdrake"
url: https://bioinfocz.github.io/scdrake
repo:
  branch: main
  url:
    home: https://github.com/bioinfocz/scdrake
    source: https://github.com/bioinfocz/scdrake/blob/master
    issue: https://github.com/bioinfocz/scdrake/issues
    user: https://github.com/bioinfocz
navbar:
  structure:
    left:  [home, intro, scdrake_integration, pipeline_overview, faq, articles, reference, news]
    right: [github]
  components:
    pipeline_overview:
      text: Pipeline overview
      href: articles/pipeline_overview.html
    scdrake_integration:
      text: Integration pipeline guide
      href: articles/scdrake_integration.html
    faq:
      text: FAQ & Howtos
      href: articles/scdrake_faq.html
articles:
  - title: Guides
    navbar: Guides
    contents:
    - scdrake_docker
    - scdrake_integration
    - scdrake_advanced
    - scdrake_extend
    - drake_basics

  - title: General information
    navbar: General information
    contents:
    - pipeline_overview
    - scdrake_faq
    - scdrake_cli
    - scdrake_config
    - scdrake_envvars

  - title: General configs
    navbar: General configs
    contents:
    - config_pipeline
    - config_main

  - title: Single-sample pipeline stages
    navbar: Single-sample pipeline stages
    contents:
    - stage_input_qc
    - stage_norm_clustering

  - title: Integration pipeline stages
    navbar: Integration pipeline stages
    contents:
    - stage_integration
    - stage_int_clustering

  - title: Common stages
    navbar: Common stages
    contents:
    - stage_cluster_markers
    - stage_contrasts
reference:
  - title: Command line interface
    desc: Install or check the command line interface.
  - contents:
    - has_concept("cli")

  - title: Project
    desc: Initialize or update a `scdrake` project.
  - contents:
    - init_project
    - update_project

  - title: Config
  - subtitle: Load or update config files
  - contents:
    - has_concept("load_config")
    - has_concept("update_config")
    - scdrake_list
  - subtitle: yq tool
    desc: Functions related to the [yq](https://github.com/mikefarah/yq) tool.
  - contents:
    - has_concept("yq_tool")

  - title: Run pipeline
  - contents:
    - has_concept("run_pipeline")
    - has_concept("create_dirs")
    - has_concept("scdrake_make")

  - title: Check for scdrake dependencies
  - contents:
    - has_concept("checks")

  - title: Get pipeline plans
  - subtitle: Full plans of the single-sample and integration pipelines
  - contents:
    - get_plan
  - subtitle: Subplans common to the single-sample and integration pipelines
  - contents:
    - has_concept("get_subplan_common")
    - has_concept("get_subplan_clustering")
    - has_concept("get_subplan_cell_annotation")
  - subtitle: Single-sample pipeline subplans
  - contents:
    - has_concept("get_subplan_single_sample")
  - subtitle: Integration pipeline subplans
  - contents:
    - has_concept("get_subplan_integration")
  - subtitle: Custom plan
  - contents:
    - load_custom_plan

  - title: Download example data
  - contents:
    - has_concept("download_example_data")

  - title: Options used by scdrake
  - contents:
    - has_concept("scdrake_options")

  - title: Target-related functions
    desc: Those functions are mostly used for individual targets within pipeline plans. They are usually named as `<target_name>_fn()`.
  - subtitle: Single-sample pipeline / stage 01_input_qc
  - contents:
    - has_concept("single_sample_input_qc_fn")
  - subtitle: Single-sample pipeline / stage 02_norm_clustering
  - contents:
    - has_concept("single_sample_norm_clustering_fn")
  - subtitle: Integration pipeline / stage 01_integration
  - contents:
    - has_concept("integration_integration_fn")

  - title: Single-cell data-related functions
  - subtitle: Annotation
  - contents:
    - has_concept("sc_annotation")
  - subtitle: Cell type annotation
  - contents:
    - has_concept("sc_cell_annotation")
  - subtitle: Cluster markers
  - contents:
    - has_concept("sc_cluster_markers")
  - subtitle: Clustering
  - contents:
    - has_concept("sc_clustering")
  - subtitle: Contrasts
  - contents:
    - has_concept("sc_contrasts")
  - subtitle: Highly variable genes (HVGs)
  - contents:
    - has_concept("sc_hvg")
  - subtitle: Markers
    desc: These functions are used in both cluster markers and contrasts stages.
  - contents:
    - has_concept("sc_markers")
  - subtitle: SingleCellExperiment object-related functions
  - contents:
    - has_concept("sc_sce")
  - subtitle: Visualization
  - contents:
    - has_concept("sce_visualization")

  - title: Misc functions
  - subtitle: HTML
  - contents:
    - has_concept("misc_html")
  - subtitle: Text
  - contents:
    - has_concept("misc_text")
  - subtitle: Utils
  - contents:
    - has_concept("misc_utils")

  - title: internal
  - contents:
    - has_concept("internal")