diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000..5008ddf Binary files /dev/null and b/.DS_Store differ diff --git a/.github/.DS_Store b/.github/.DS_Store new file mode 100644 index 0000000..d608945 Binary files /dev/null and b/.github/.DS_Store differ diff --git a/.github/workflows/make-mkdocs.yaml b/.github/workflows/make-mkdocs.yaml new file mode 100644 index 0000000..b334545 --- /dev/null +++ b/.github/workflows/make-mkdocs.yaml @@ -0,0 +1,21 @@ +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 diff --git a/README.md b/README.md index 3d37058..fdc5426 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,7 @@ -# cnv-reference-resources -Data & tools for hCNV analysis with a focus on the distributed normal +# 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) \ No newline at end of file diff --git a/docs/beacon-queries.md b/docs/beacon-queries.md new file mode 100644 index 0000000..9fcab84 --- /dev/null +++ b/docs/beacon-queries.md @@ -0,0 +1,3 @@ +# Beacon CNV Queries + +==TBD== \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index c97182f..3009473 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1 +1,61 @@ -site_name: My Docs +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: + - Home: / + - Topic Pages: + - Input Data: data-resources + - Parameters & Mappings: parameters-and-mappings + - Beacon Queries: beacon-queries + - 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