DPIPE documentation

Welcome to DPIPE documentation.

Here you will find documentation relevant for our DPIPE and alleles repositories, including procedures/how-to guides, system overviews and explanations, as well as description and reference docs from different repositories.

Please use the navigation menu on the left or use search (keyboard shortcut /) to find what you are looking for.

How this documentation site works

The document source files come from the repository docs-store, as well as from all other repositories that have documentation and are included in the configuration. The docs are gathered by the docs-builder (1-4), which uses MkDocs with Material to build the docs to HTML (5) before they are pushed to docs-pages (6) and end up here (8).

sequenceDiagram
autonumber
participant docsbuilder
participant docsstore
participant otherrepo
participant docspages
participant Gitlabpages

docsbuilder ->> docsstore : Get general docs
docsstore -->> docsbuilder : source files
docsbuilder ->> otherrepo : Get repo-specific docs
otherrepo -->> docsbuilder : source files
docsbuilder ->> docsbuilder : Build diagrams (PlantUML) and docs (MkDocs)
docsbuilder ->> docspages : Push HTML to /public
docspages ->> docspages : Run CI job "pages"
docspages ->> Gitlabpages : Publish docs

Use relative links when linking to other docs, images etc. All repos, including docs-store, are available one level below the repo root directory you are linking from. For example, to link from docs-store/docs/somefolder/somefile.md to vcpipe/doc/pipelines.md, you can in somefile.md point to ../../../../vcpipe/doc/pipelines.md