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mkdocs.yaml
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mkdocs.yaml
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site_name: Poppy
nav:
- Overview:
- Introduction: intro.md
- Pipeline overview: overview.md
- Output: output_files.md
- Setup and configuration: setup.md
- Running Poppy:
- Poppy: poppy.md
- Reference pipeline: reference_files.md
- Step-by-step:
- Pre-alignment: prealignment.md
- Alignment: alignment.md
- SNV and indels: snvs.md
- CNVs: cnvs.md
- QC: qc.md
- Pipeline specific rules:
- Software: softwares.md
- Project info:
- Changelog: changelog.md
theme: readthedocs
extra_css: [extra.css]
markdown_extensions:
- abbr
- attr_list
- pymdownx.details
- pymdownx.snippets:
auto_append:
- includes/abbreviations.md
base_path: ["docs/", "workflow/rules/"]
url_download: "True"
# - mdx_spanner
- admonition
- pymdownx.emoji:
emoji_index: !!python/name:materialx.emoji.twemoji
emoji_generator: !!python/name:materialx.emoji.to_svg
- pymdownx.blocks.details
plugins:
- search
- include-markdown
- 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"