mkdocs.yml

site_name: Twist Solid
nav:
  - Overview:
    - Introduction: index.md
    - Pipeline overview: overview.md
    - Result files: result_files.md
    - Pipeline setup and configuration: setup.md
    - Reference files: references.md
  - Running the pipeline:
    - Basic: running.md
    - Restricted system: run_on_restricted_system_env.md
    - Bianca: run_on_bianca.md
  - DNA Pipeline:
    - Pre-alignment: dna_prealignment.md
    - Alignment: dna_alignment.md
    - SNV and INDELs: dna_snv_indels.md
    - CNVs: dna_cnvs.md
    - Fusions: dna_fusions.md
    - Biomarkers: dna_biomarkers.md
    - QC: dna_qc.md
  - RNA Pipeline:
    - Fusions: rna_fusions.md
    - Exon skipping: rna_exon_skipping.md
    - ID-SNPs: rna_id_snps.md
    - QC: rna_qc.md
  - Pipeline specific rules:
    - Rule list: softwares.md
  - Project Info:
    - Changelog: changelog.md
    - Citations: citations.md
    - Contributing: contributing.md
    - Credits: credits.md
    - Frequently Asked Questions: faq.md
    - License: license.md
    - More Resources: more_resources.md


theme:
    name: readthedocs
extra_css: [extra.css]
markdown_extensions:
  - abbr
  - admonition
  - attr_list
  - mdx_spanner
  - pymdownx.blocks.details
  - pymdownx.snippets:
      auto_append:
        - includes/abbreviations.md
      base_path: "docs/"
      url_download: "True"
  - pymdownx.emoji:
      emoji_index: !!python/name:materialx.emoji.twemoji
      emoji_generator: !!python/name:materialx.emoji.to_svg
  - toc:
      permalink: True

plugins:
  - include-markdown
  - search
  - yaml-schema:
      yaml_files:
        - file: "workflow/schemas/config.schema.yaml"
          tag: "CONFIGSCHEMA"
        - file: "workflow/schemas/resources.schema.yaml"
          tag: "RESOURCESSCHEMA"
  - snakemake-rule:
      rule_folders:
        - 'workflow/rules'
      schemas:
        - 'workflow/schemas/rules.schema.yaml'
  - mkdocs-simple-hooks:
      hooks:
        on_pre_build: "docs.hooks:copy_changelog_and_license"