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 |