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/Status-systems.md |
not in EHB |
Status for GDx-bioinf systems |
| Development/Status-datasets.md |
not in EHB |
Status for datasets and settings used in GDx-bioinf pipelines |
| Development/Development-and-review.md |
93790 |
Software 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 |
| Development/System-owner-checklist.md |
not in EHB |
System owner checklist |
| 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-development-requests.md |
148124 |
Development requests to GDx |
| Production-routines/Helpdesk-process.md |
not in EHB |
Process for the bioinformatic helpdesk |
| Production-routines/Use-of-Teams-ops-channel.md |
not in EHB |
Use of GDx operational channel in Teams |
System - automation
| docs-store |
eHB id |
title |
| 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 |
| Production-routines/Scheduled-recurring-jobs.md |
- |
Scheduled recurring jobs |
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 |
title |
| 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 |
| User-guides/ELLA-CNV-module-analytic.md |
143594 |
ELLA CNV module: CNV calling and filtering |
| User-guides/ELLA-MT-module.md |
142884 |
ELLA MT module |
| 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 of in-house annotation data |
| Annotation-and-reference-data-updates/Update-of-external-annotation-data.md |
107120 |
Update of external annotation data |
| 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