mkdocs based project documentation site

.github/workflows/make-mkdocs.yaml

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+name: mk-docs 
+on:
+  push:
+    branches:
+      - main
+      - master
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+      - run: pip install mkdocs-material 
+      - run: pip install mkdocs-macros-plugin
+      - run: pip install pymdown-extensions
+      - run: pip install mkdocs-mermaid2-plugin
+      - run: pip install mdx_gh_links
+      - run: pip install mkdocs-with-pdf
+      - run: mkdocs gh-deploy --force

README.md

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+# [hCNV Reference Resources](https://cnvar.org/cnv-reference-resources/)
+
+**Data & tools for hCNV analysis with a focus on the distributed normal**
+
+The site was started as a project of the [ELIXIR hCNV Community](https://cnvar.org)
+at the [Biohackathon Europe 2023](https://biohackathon-europe.org):
+
+**[A "batteries-included" open reference resource for human genomic copy number variants (CNV)](https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/1)**
+
+This sitecan be found at [cnvar.org/cnv-reference-resources/](https://cnvar.org/cnv-reference-resources/).

docs/beacon-queries.md

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+# Beacon CNV Queries
+
+! hint "Beacon Project Query Documentation"
+
+    The Beacon [project's documentation](http://docs.genomebeacons.org/variant-queries/#beacon-range-queries) includes examples for current queries enabling
+    discovery of CNVs (in resources supporting these formats).
+
+
+==TBD==

docs/data-resources.md

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+# hCNV Reference Data Resources
+
+## 1000 Genomes Dragen
+
+While primarily focused on somatic variants from cancer genomics the Progenetix
+resource also contains [CNV data from the 1000 Genomes Project](https://aws.amazon.com/blogs/industries/dragen-reanalysis-of-the-1000-genomes-dataset-now-available-on-the-registry-of-open-data/).
+
+* [1000 Genomes CNV](https://progenetix.org/progenetix-cohorts/oneKgenomes/) at Progenetix
+
+==TBD==

docs/index.md

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+# hCNV Reference Resources
+##### Data & tools for hCNV analysis with a focus on the distributed normal
+
+The site was started as a project of the [ELIXIR hCNV Community](https://cnvar.org)
+at the [Biohackathon Europe 2023](https://biohackathon-europe.org):
+
+**[A "batteries-included" open reference resource for human genomic copy number variants (CNV)](https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/1)**
+

docs/parameters-and-mappings.md

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+# hCNV Parameters and Mappings to Output format
+
+## Collected Parameters
+
+==TBD==
+
+## Parameter Output Mappings
+
+### Beacon v2 Default Model for `genomicVariation`
+
+* [**Beacon v2 default model source**](https://github.com/ga4gh-beacon/beacon-v2/tree/main/models/src/beacon-v2-default-model)
+* [**Beacon v2 default model documentation**](http://docs.genomebeacons.org/models/)
+
+Beacon v2 provides a default model with its main data entities `individual`,
+`biosample`, `analysis`, `run` and `genomicVariation`. The parameters needed for
+an hCNV reference resource potentially map to all of those entities; e.g.
+
+* donor sex  => `individual.sex`
+
+

mkdocs.yml

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+site_name: hCNV Reference Resources
+site_description: 'Data & tools for hCNV analysis with a focus on the distributed normal'
+site_author: Michael Baudis
+repo_name: 'cnv-reference-resources'
+repo_url: https://github.com/hCNV/cnv-reference-resources
+edit_uri: edit/main/docs/
+
+###############################################################################
+
+nav:
+  - Project Home: index
+  - Input Data: data-resources
+  - Parameters & Mappings: parameters-and-mappings
+  - Beacon Queries: beacon-queries
+  - hCNH Home: /
+  - Biohack 2023 Page: https://github.com/elixir-europe/biohackathon-projects-2023/tree/main/1
+  - Beacon Documentation: 'https://docs.genomebeacons.org'
+
+###############################################################################
+
+markdown_extensions:
+  - toc:
+      toc_depth: 2-3
+      permalink: true
+  - admonition
+  - attr_list
+  - footnotes
+  - md_in_html
+  - pymdownx.critic
+  - pymdownx.caret
+  - pymdownx.details
+  - pymdownx.keys
+  - pymdownx.magiclink:
+      hide_protocol: true
+  - pymdownx.mark
+  - pymdownx.tilde
+  - pymdownx.saneheaders
+  - pymdownx.superfences:
+      custom_fences:
+        - name: mermaid
+          class: mermaid
+          format: !!python/name:mermaid2.fence_mermaid   
+  - pymdownx.tabbed:
+      alternate_style: true
+  - pymdownx.tasklist:
+      custom_checkbox: true
+  - tables
+  - mdx_gh_links:
+      user: hCNV
+      repo: hcnv.github.io
+  - pymdownx.emoji:
+        emoji_index: !!python/name:materialx.emoji.twemoji
+        emoji_generator: !!python/name:materialx.emoji.to_svg
+
+###############################################################################
+
+theme:
+  name: material
+plugins:
+    - search
+    - macros