Clinical-Genomics/scout issues and pull requests

#4723 - Implement oauth for igv.js

Issue - State: closed - Opened by northwestwitch 2 months ago - 1 comment
Labels: enhancement

#4722 - Hovertip to gene panel names with associated genes on SV variant page

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 14 comments
Labels: Customer Request, Easy

#4721 - Option to override the ClinVar API URL to test against ClinVar 'apitest'

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 2 comments
Labels: enhancement

#4720 - dbVar track unreachable?

Issue - State: closed - Opened by northwestwitch 2 months ago - 3 comments

#4719 - Un-audit filter

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 4 comments
Labels: enhancement, QualityOfLife

#4718 - Missing OMIM entries on variant page, which are present in hover

Issue - State: closed - Opened by Jakob37 2 months ago - 21 comments
Labels: question

#4717 - Minor version 4.85

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 5 comments

#4716 - Try to convert to float only GNOMAD POPMAX values that are numerical

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 2 comments

#4715 - Replace broken "remove" icon

Pull Request - State: closed - Opened by northwestwitch 2 months ago - 5 comments
Labels: Easy, Bugfix, Frontend

#4714 - Failing to parse "GNOMADE_POPMAX"

Issue - State: closed - Opened by Jakob37 2 months ago - 10 comments

#4713 - NOt possible to DELETE a comment

Issue - State: closed - Opened by 4WGH 3 months ago - 7 comments
Labels: bug

#4712 - HGNC symbols not present in database's genes collection:{'MAP3K20'}

Issue - State: closed - Opened by alieden 3 months ago - 2 comments
Labels: question

#4711 - Cases advanced search

Pull Request - State: open - Opened by northwestwitch 3 months ago - 4 comments
Labels: enhancement, Customer Request

#4710 - REVEL score deep parsing

Pull Request - State: closed - Opened by northwestwitch 3 months ago - 9 comments
Labels: enhancement

#4709 - Display removed panels for commoners

Pull Request - State: closed - Opened by northwestwitch 3 months ago - 8 comments
Labels: Customer Request

#4708 - Display samples' name and affected status directly on caseS page

Pull Request - State: closed - Opened by northwestwitch 3 months ago - 2 comments
Labels: Easy

#4707 - Address request.redirect security issue raised by CodeQL

Issue - State: open - Opened by northwestwitch 3 months ago
Labels: enhancement, Task

#4706 - Show sample ids of at least affected individual on the caseS page

Issue - State: closed - Opened by dnil 3 months ago
Labels: enhancement, Customer Request, QualityOfLife

#4705 - Highlight search result on caseS page, especially wrt prioritised cases

Issue - State: open - Opened by dnil 3 months ago - 3 comments
Labels: enhancement, Customer Request

#4704 - Advanced case search

Issue - State: open - Opened by dnil 3 months ago
Labels: enhancement, Customer Request

#4703 - MT (eklipse) display in Scout with RareDisease pipeline

Issue - State: closed - Opened by Lucpen 3 months ago - 5 comments
Labels: wontfix

#4702 - In Scout DROP results are viewed with ACC numbers

Issue - State: closed - Opened by Lucpen 3 months ago - 3 comments
Labels: Under discussion

#4701 - Download DROP results from Scout

Issue - State: closed - Opened by Lucpen 3 months ago - 3 comments
Labels: enhancement, Easy

#4700 - view Tomte VCF in Scout

Issue - State: open - Opened by Lucpen 3 months ago - 8 comments
Labels: enhancement, blocked

#4699 - Show (Removed) after removed panels in dropdown

Pull Request - State: closed - Opened by Jakob37 3 months ago - 4 comments

#4698 - Indicate in panel drop-downs which panels are removed

Issue - State: closed - Opened by Jakob37 3 months ago - 1 comment
Labels: enhancement

#4697 - Sort select default

Pull Request - State: closed - Opened by dnil 3 months ago - 8 comments
Labels: Easy, Bugfix

#4696 - Allow toggling display of hidden panels for normal users

Issue - State: closed - Opened by Jakob37 3 months ago - 2 comments
Labels: enhancement

#4695 - Removed panels are displayed on case page

Issue - State: closed - Opened by Jakob37 3 months ago - 9 comments
Labels: bug, enhancement

#4694 - Tooltips for Tomte outliers view

Issue - State: closed - Opened by dnil 3 months ago
Labels: enhancement, Easy

#4693 - REVEL score not reported if not present in the first CSQ-field transcript

Issue - State: closed - Opened by Jakob37 3 months ago - 4 comments
Labels: enhancement

#4692 - SV gene variantS search

Pull Request - State: closed - Opened by dnil 3 months ago - 4 comments

#4691 - Fix #4688 - unfreeze werkzeug to finally get >v3.0

Pull Request - State: closed - Opened by dnil 3 months ago - 3 comments

#4690 - Add MSI score for tumor-normal cases

Issue - State: closed - Opened by khurrammaqbool 3 months ago - 1 comment

#4689 - [obophenotype/human-phenotype-ontology] Release 2024-07-01

Issue - State: closed - Opened by dnil 3 months ago - 2 comments
Labels: Task

#4688 - Unfreeze Werkzeug again

Issue - State: closed - Opened by dnil 3 months ago
Labels: enhancement

#4687 - Version 4.84 - fix load order, chanjo-report extension load warning, …

Pull Request - State: closed - Opened by dnil 3 months ago - 5 comments

#4686 - How we calculate VAF in scout

Issue - State: open - Opened by northwestwitch 4 months ago - 1 comment
Labels: question, Customer Request

#4685 - Linter python versions

Pull Request - State: closed - Opened by dnil 4 months ago - 3 comments

#4684 - Workaround fix #4682 - sort case file load order alphabetically

Pull Request - State: closed - Opened by dnil 4 months ago - 3 comments

#4683 - Swap menu chevrons

Pull Request - State: closed - Opened by dnil 4 months ago - 2 comments

#4682 - SV variants and large SNVs collide in variant_id

Issue - State: closed - Opened by dnil 4 months ago
Labels: bug

#4681 - Stylistic updates to the "calculate matching causatives" toggle

Issue - State: closed - Opened by Jakob37 4 months ago

#4680 - Fix gene links

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 2 comments
Labels: Easy, Bugfix

#4679 - Link to HGNC portal broken on gene page

Issue - State: closed - Opened by northwestwitch 4 months ago
Labels: bug

#4678 - Pydantic gene

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 6 comments
Labels: Easy, Refactor

#4677 - Load genes missing Ensembl ID using cytoband coordinates

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 4 comments

#4676 - Clearer chanjo-report error message only when needed

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 3 comments
Labels: Easy

#4675 - Import chanjo-report warning emitted before log level set

Issue - State: closed - Opened by dnil 4 months ago
Labels: QualityOfLife, Refactor

#4674 - Safer variant updates in variantS controllers

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 2 comments
Labels: Easy, Refactor, Bugfix

#4673 - Flash an alert when loqus instance is not reachable

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 4 comments

#4672 - nf-core/raredisease MT variants loading

Issue - State: closed - Opened by dnil 4 months ago - 4 comments

#4671 - Upgrade python to 3.11 in the Dockerfiles

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 3 comments

#4670 - When updating the OMIM panel with --force, update also the date

Issue - State: closed - Opened by northwestwitch 4 months ago - 2 comments
Labels: QualityOfLife

#4669 - Warnings when loqusdb-api is not reachable

Issue - State: closed - Opened by dnil 4 months ago
Labels: enhancement

#4668 - Extremely slow loading of variant pages when loqusdb instance can't be reached

Issue - State: closed - Opened by northwestwitch 4 months ago - 3 comments

#4667 - Minor release 4.83

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 17 comments

#4666 - CLI option to link a panel to multiple institutes

Issue - State: closed - Opened by Jakob37 4 months ago - 6 comments

#4665 - CLI option to remove an institute

Issue - State: open - Opened by Jakob37 4 months ago - 4 comments
Labels: enhancement, Intermediate

#4664 - Changelog reminder version

Pull Request - State: closed - Opened by dnil 4 months ago - 7 comments

#4663 - Automation: check CHANGELOG changes for latest version/unreleased

Issue - State: open - Opened by dnil 4 months ago
Labels: enhancement, QualityOfLife

#4662 - Fix automatically loading research variants when loading a case

Pull Request - State: closed - Opened by northwestwitch 4 months ago - 5 comments
Labels: Easy, Bugfix

#4661 - "scout setup demo" is loading also research variants, but they are not shown as a category of available vars on case page

Issue - State: closed - Opened by northwestwitch 4 months ago - 2 comments
Labels: bug

GitHub / Clinical-Genomics/scout issues and pull requests