From 1da77276b398f3199da7b3f6e52acdc341a65c41 Mon Sep 17 00:00:00 2001 From: Michael Baudis Date: Sun, 29 Oct 2023 07:59:24 +0100 Subject: [PATCH] mkdocs based project documentation site --- .DS_Store | Bin 0 -> 6148 bytes .github/.DS_Store | Bin 0 -> 6148 bytes .github/workflows/make-mkdocs.yaml | 21 ++++++++++ README.md | 10 +++++ docs/beacon-queries.md | 9 +++++ docs/data-resources.md | 10 +++++ docs/index.md | 8 ++++ docs/parameters-and-mappings.md | 20 ++++++++++ mkdocs.yml | 61 +++++++++++++++++++++++++++++ 9 files changed, 139 insertions(+) create mode 100644 .DS_Store create mode 100644 .github/.DS_Store create mode 100644 .github/workflows/make-mkdocs.yaml create mode 100644 README.md create mode 100644 docs/beacon-queries.md create mode 100644 docs/data-resources.md create mode 100644 docs/index.md create mode 100644 docs/parameters-and-mappings.md create mode 100644 mkdocs.yml diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6 GIT binary patch literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0 zI0MeWj~T$7Ez(RCy>|wj0cYTg0XZK6nqV}{isk4)S4se&Jfn+1ms&!6f?+hwidccL zx&qaet;Aq;$9yomXqXk%o!E*Gww*tV7cRRaekkU|QPF#6z!?}baH+$Y-2Y4bGSwn~ z?BXM5z!~^w4Dh5~wF`Wd-K}SzCwFZ?yG0WbyDSO>`sfjWft(}PWl`6I=&*~1Sy7_M Sd~pZ*L!c1ioip$Y4155>k2JXe literal 0 HcmV?d00001 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 new file mode 100644 index 0000000..47b0be3 --- /dev/null +++ b/README.md @@ -0,0 +1,10 @@ +# [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/). \ No newline at end of file diff --git a/docs/beacon-queries.md b/docs/beacon-queries.md new file mode 100644 index 0000000..fcd9b1f --- /dev/null +++ b/docs/beacon-queries.md @@ -0,0 +1,9 @@ +# 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== \ No newline at end of file diff --git a/docs/data-resources.md b/docs/data-resources.md new file mode 100644 index 0000000..05e54f0 --- /dev/null +++ b/docs/data-resources.md @@ -0,0 +1,10 @@ +# 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== \ No newline at end of file diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..7f81d15 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,8 @@ +# 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)** + diff --git a/docs/parameters-and-mappings.md b/docs/parameters-and-mappings.md new file mode 100644 index 0000000..7e5f795 --- /dev/null +++ b/docs/parameters-and-mappings.md @@ -0,0 +1,20 @@ +# 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` + + diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..708c6e1 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,61 @@ +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