docs-store

All documentation not belonging in other specific repos.

This project will contain all documentation that does not belong in the /docs directory of other repositories. The plan is to use this repo for all documentation that is currently in eHåndbok, and also clean up and move the wiki here. The docs-store repo will be one of the larger sources for docs-builder which will gather documentation from this and other repositories and build a single web page with all documentation and diagrams.

List of procedures, ehåndbok and systems can be found below. Note that the procedures marked not in EHB are internal documents not contained in EHB, all other documents must exist (or be created) in EHB.

System - docs

docs-store	eHB id	title
Overview-and-organisation/Bioinformatics-group-roles.md	125147	Bioinf Group roles
Overview-and-organisation/ Project-management-and-agile.md	not in EHB	Overall process of work organisation
Overview-and-organisation/About-our-documentation.md	146764	Documentation overview
Overview-and-organisation/How-to-update-EHB.md	146765	Update of procedures in e-håndbok
Overview-and-organisation/How-to-update-docs-webpages.md	146851	Update of the central docs web-pages
Overview-and-organisation/Employee-onboarding-routines.md	not in EHB	Employee onboarding routines
Systems_overview/Systems-overview.md	-	to be written
Development/Development-and-review.md	93790	Development and review
Development/Issue-management.md	not in EHB	Issue management
Development/How-to-start-new-Gitlab-project-repo.md	not in EHB	How to start a new Gitlab project repo

System - automation

docs-store	eHB id	system
Infrastructure-and-data-management/Infrastructure.md	123214	Infrastructure
Infrastructure-and-data-management/User_accounts_management.md	-	to be written
Infrastructure-and-data-management/Storage-and-security-of-sensitive-data.md	93827	Storage and security of sensitive data
Infrastructure-and-data-management/Software-administration.md	96746	Software administration
Infrastructure-and-data-management/File-system-usage-and-locations.md	-	to be written
Infrastructure-and-data-management/nipt-hardware-and-infrastructure.md	143745	NIPT Hardware and IT Infrastructure
Releases-and-production-system-updates/Release-and-deployment-of-TSD-import.md	93782	Release and deployment of tsd-import

System - variant calling

docs-store	eHB id	title
Training-procedures/Training-for-running-pipeline.md	93592	Training for running pipeline
Analysis-and-pipeline-specifications/Basepipe-specification.md	137607	Basepipe pipeline
Analysis-and-pipeline-specifications/Triopipe-specification.md	99571	Trio pipeline
Analysis-and-pipeline-specifications/NIPT-specification.md	143744	NIPT Software
Analysis-and-pipeline-specifications/CNV-exome-targeted-specification.md	125544, rename	Copy Number Variation in exome pipelines
Releases-and-production-system-updates/Release-and-deployment-of-vcpipe.md	91296	Deployment of vcpipe for production
Releases-and-production-system-updates/Process-for-updates-to-production-pipelines.md	93783	Process for updates to production pipelines
Releases-and-production-system-updates/Using-the-vcpipe-staging.md	146831	Using the vcpipe staging environment
Quality-control-monitoring-and-error-handling/Demultiplexing-and-qc-of-raw-seq-data.md	106057	Demultiplexing and quality control of raw sequencing data
Production-routines/Execution-and-monitoring-of-pipeline.md	91091	Execution and monitoring of pipeline
Production-routines/Use-of-service-user.md	146799	Using service user
Gene-panel-and-region-configuration/Create-region-files-for-new-capture-kits.md	125003	Create region files for the new capture kit

System - annotation

docs-store	eHB id	system
Analysis-and-pipeline-specifications/Variant-filtering-upstream-of-ELLA.md	-	to be written
Analysis-and-pipeline-specifications/Anno-with-anno-targets.md	133295	Anno with anno-targets
Releases-and-production-system-updates/Release-and-deployment-of-anno.md	146769	Release and deployment of anno system
Annotation-and-reference-data-updates/Update-of-sensitive-annotation-data.md	116906	Update sensitive databases
Annotation-and-reference-data-updates/Update-of-public-annotation-data.md	107120, rename	Update Databases
Annotation-and-reference-data-updates/Update-of-Convading-background-data.md	136591	Convading background data
Production-routines/Running-anno.md	146770	Running annoservice

System - interpretation

docs-store	eHB id	system
Training-procedures/Training-for-ELLA-core-developers.md	134772	Training for ELLA core developers
Production-routines/ELLA-production.md	128961	ELLA production
Production-routines/ELLA-core-production.md	134813	ELLA core production
Gene-panel-and-region-configuration/Create-region-files-for-new-capture-kits.md	125003, rewrite	Create region files for the new capture kit
Gene-panel-and-region-configuration/Create-and-change-genepanel-files.md	91377, rewrite	Create and change gene panel files
Gene-panel-and-region-configuration/Coverage-check-of-gene-panels.md	93706, rewrite	Coverage check of gene panels