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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 Bioinformatics 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 - draft
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
Production-routines/Service-level-agreement.md 147443 Serviceerklaring - Enhet for genomdiagnistikk
Production-routines/Helpdesk-user-info.md 149082 User information page for GDx-bioinf helpdesk
Production-routines/Helpdesk-process.md not in EHB Process for the bioinformatic helpdesk

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