Ecosyste.ms: Issues

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GitHub / Clinical-Genomics/scout issues and pull requests

#4415 - Fix show matching partial causatives on variant page

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 2 comments

#4414 - Enhance log output when VEP transcript variant frequency parsing fails

Pull Request - State: closed - Opened by alkc 8 months ago - 3 comments

#4413 - GnomAD LOEUF

Pull Request - State: closed - Opened by dnil 8 months ago - 9 comments

#4412 - Fix show matching causatives

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 4 comments

#4411 - question on panel version

Issue - State: closed - Opened by 4WGH 8 months ago - 4 comments
Labels: question

#4408 - Connection failure warning when you run scout --help command

Issue - State: closed - Opened by northwestwitch 8 months ago - 4 comments
Labels: bug, wontfix

#4407 - Replace schug dependency with requests to schug web

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 4 comments
Labels: Easy, Bugfix, blocked

#4406 - Add more helpful error message when variant frequency parsing fails in `scout.parse.variant.transcript`

Issue - State: closed - Opened by alkc 8 months ago - 1 comment
Labels: enhancement, Easy

#4405 - Error while executing scout after a fresh conda installation - ARM processor

Issue - State: closed - Opened by northwestwitch 8 months ago
Labels: question, wontfix

#4404 - Attempt at fixing gunicorn boot

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 1 comment

#4403 - Can't deploy newly-built images on cg-vm1 - Gunicorn error. again

Issue - State: closed - Opened by northwestwitch 8 months ago - 7 comments
Labels: bug

#4402 - Chanjo2 report for cases with d4 files

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 42 comments

#4401 - Matching causative not shown

Issue - State: closed - Opened by MUebe 8 months ago - 4 comments
Labels: bug

#4400 - Block and then refactor submission of somatic variants to ClinVar

Issue - State: open - Opened by northwestwitch 8 months ago
Labels: enhancement

#4399 - Refactor `build_case()` and `CaseLoader`

Issue - State: open - Opened by dnil 8 months ago
Labels: Refactor

#4398 - Update command that downloads ORPHA data to include inheritance file

Issue - State: closed - Opened by northwestwitch 8 months ago
Labels: enhancement

#4397 - Unable to parse HGNC ID due to presence of 'HGNC:' prefix

Issue - State: closed - Opened by lfearnley 8 months ago - 5 comments
Labels: nf-core/raredisease

#4396 - Relax standard output on CLI

Issue - State: closed - Opened by dnil 8 months ago
Labels: enhancement, QualityOfLife

#4395 - Allow `poorpipe` long read sequencing uploads

Issue - State: closed - Opened by dnil 8 months ago - 4 comments
Labels: enhancement, LRS

#4394 - Rename "Clinical significance" to "Germline classification" in ClinVar variant files

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 5 comments
Labels: Bugfix

#4392 - Update ClinVar inheritance models according to changed ClinVar API

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 2 comments
Labels: Easy

#4391 - Many breaking changes in the new ClinVar submission sheets

Issue - State: closed - Opened by northwestwitch 8 months ago - 2 comments
Labels: bug

#4388 - Fix remaining relative paths on load

Pull Request - State: closed - Opened by dnil 8 months ago - 12 comments

#4387 - Stop supporting ClinVar submission using CSV files and submit only using the API

Issue - State: open - Opened by northwestwitch 8 months ago
Labels: Future ideas, QualityOfLife, Refactor, Task

#4386 - Fix ClinVar condition IDs format (add prefix in background)

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

#4385 - Wrong condition ID format for ORPHA terms

Issue - State: closed - Opened by northwestwitch 8 months ago
Labels: bug

#4384 - Loqusdbapi only in this "case"

Issue - State: closed - Opened by dnil 8 months ago
Labels: enhancement, Easy, Task

#4383 - Revert style of pinned variants window on case page

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 2 comments

#4382 - Case page pinned vars layout..

Issue - State: closed - Opened by dnil 8 months ago - 4 comments
Labels: Frontend

#4381 - Fix diseases associated to partial causatives (style, links)

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 4 comments
Labels: Easy, Frontend

#4380 - Updated styling of case_report to align card contents and headers

Pull Request - State: closed - Opened by TereseBo 8 months ago - 3 comments

#4379 - Associate ClinVar variants with Orphanet conditions

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

#4377 - Introduce a super-simple ClinVar multistep validation system and validate associated condition

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

#4376 - Subject id and phenotype groups

Pull Request - State: closed - Opened by dnil 8 months ago - 5 comments

#4375 - Partial causatives-associated diseases not visible on case page

Issue - State: closed - Opened by northwestwitch 8 months ago
Labels: Easy, Frontend

#4374 - ClinVar HPO-terms only rarely possible as condition for the classification

Issue - State: closed - Opened by dnil 8 months ago - 3 comments
Labels: enhancement

#4373 - ClinVar submission: warn when not filling disorder

Issue - State: closed - Opened by dnil 8 months ago - 4 comments
Labels: enhancement

#4372 - Display ORPHA codes on diagnoses page

Issue - State: closed - Opened by northwestwitch 8 months ago - 1 comment
Labels: enhancement

#4371 - Add inheritance to orpha

Pull Request - State: closed - Opened by TereseBo 8 months ago - 3 comments

#4370 - Fix number of phenotypes and genes from case diagnoses

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

#4369 - Alamut linkout documentation

Issue - State: open - Opened by dnil 8 months ago
Labels: enhancement, docs

#4368 - Error while updating genes

Issue - State: closed - Opened by northwestwitch 8 months ago - 1 comment

#4367 - Diagnosis HPO and gene count 0..

Issue - State: closed - Opened by dnil 8 months ago
Labels: bug

#4366 - Some cases don't have the Diagnoses section

Issue - State: closed - Opened by northwestwitch 9 months ago - 4 comments
Labels: bug

#4364 - Remove capital letters from descriptions of ClinVar events on case page

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

#4363 - Update individual's path to .d4 files for an existing case

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

#4362 - Remove the unused no-variants param from load_case cli

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

#4361 - Associate .d4 files to individuals when loading a case via config file

Pull Request - State: closed - Opened by northwestwitch 9 months ago - 2 comments
Labels: enhancement, Easy

#4359 - Fix #3937 - case status tags

Pull Request - State: closed - Opened by dnil 9 months ago - 4 comments

#4358 - New minor version 4.76

Pull Request - State: closed - Opened by northwestwitch 9 months ago - 7 comments

#4356 - Frontend for orphacodes

Pull Request - State: closed - Opened by TereseBo 9 months ago - 8 comments

#4355 - Show user that created a ClinVar submission, when available

Pull Request - State: closed - Opened by northwestwitch 9 months ago - 2 comments
Labels: Easy

#4354 - Genes for orpha disease_terms are now saved as int, matching the format for omim disease_terms

Pull Request - State: closed - Opened by TereseBo 9 months ago - 3 comments
Labels: Easy

#4353 - Fix Pop Freq Cancer SV Variants View

Pull Request - State: closed - Opened by ivadym 9 months ago - 6 comments

#4352 - Missing BAM files and chromograph

Issue - State: closed - Opened by Leif-glitch 9 months ago - 2 comments

#4351 - Allow ClinVar submissions with custom API keys and allow resetting submission ID

Pull Request - State: closed - Opened by northwestwitch 9 months ago - 2 comments
Labels: Easy, QualityOfLife

#4349 - somatic view variantS archive variants filtering

Issue - State: closed - Opened by dnil 9 months ago
Labels: enhancement, Cancer

#4348 - Fix archived local obs not visible on cancer variantS page

Pull Request - State: closed - Opened by northwestwitch 9 months ago - 4 comments
Labels: Easy, Bugfix

#4347 - Remove unused parameter in server/blueprints/variant/controllers/observations

Pull Request - State: closed - Opened by northwestwitch 9 months ago - 2 comments
Labels: Easy

#4346 - Update diagnosis page

Pull Request - State: closed - Opened by TereseBo 9 months ago - 4 comments

#4345 - Sanger feedback

Pull Request - State: closed - Opened by northwestwitch 9 months ago - 4 comments
Labels: Customer Request

#4343 - Fix sumenu icon fa5

Pull Request - State: closed - Opened by dnil 9 months ago - 1 comment

#4342 - Enable Cancer SV observations view

Pull Request - State: closed - Opened by ivadym 9 months ago - 6 comments
Labels: Bugfix

#4341 - Missing views for Cancer SVs

Issue - State: closed - Opened by ivadym 9 months ago - 7 comments
Labels: bug

#4339 - submenu icon gone missing..

Issue - State: open - Opened by dnil 9 months ago - 1 comment

#4338 - GnomAD 38 v4 links

Pull Request - State: closed - Opened by dnil 9 months ago - 2 comments

#4337 - Fix removing the same ClinVar variant from 2 different tabs

Pull Request - State: closed - Opened by northwestwitch 9 months ago - 2 comments
Labels: Bugfix

#4336 - Fix None search as default case search in cases form

Pull Request - State: closed - Opened by northwestwitch 9 months ago - 6 comments
Labels: Easy, Bugfix

#4335 - Empty cases side after clicking "Search"

Issue - State: closed - Opened by Jakob37 9 months ago - 3 comments
Labels: duplicate

#4334 - Gnomad link to point to v4 for SNVs

Issue - State: closed - Opened by Jakob37 9 months ago - 2 comments
Labels: bug

#4332 - New HPO release 2024-01-11

Issue - State: closed - Opened by northwestwitch 9 months ago - 5 comments
Labels: Clinical Genomics Solna instance only, Task

#4331 - Loqus DB links to homozygous cases

Issue - State: open - Opened by Jakob37 9 months ago - 2 comments
Labels: enhancement, Intermediate

#4329 - Add XTR region to PAR region definition?

Issue - State: closed - Opened by dnil 9 months ago
Labels: enhancement

#4328 - question about spliceAI

Issue - State: open - Opened by 4WGH 9 months ago - 1 comment
Labels: question

#4327 - Removing variant from clinvar submission crash

Issue - State: closed - Opened by dnil 9 months ago - 1 comment
Labels: bug

#4326 - Display user responsible for adding to ClinVar subs on the submission list

Issue - State: closed - Opened by dnil 9 months ago - 5 comments
Labels: enhancement, QualityOfLife

#4324 - Allow users to add additional API-key

Issue - State: closed - Opened by dnil 9 months ago
Labels: QualityOfLife

#4323 - Fix #4322 - ClinVar submitters cleared with unpriv saving

Pull Request - State: closed - Opened by dnil 9 months ago - 2 comments
Labels: Bugfix

#4321 - Matching partial causatives view on the variant page

Issue - State: closed - Opened by dnil 9 months ago - 2 comments
Labels: bug

#4320 - Cannot chose newly added gene panel

Issue - State: closed - Opened by ielvers 9 months ago - 6 comments
Labels: question, Customer Request

#4319 - Validate custom image paths when a case is loaded

Pull Request - State: closed - Opened by northwestwitch 9 months ago - 2 comments
Labels: Easy

#4318 - Customise institute settings to be able to display all cases with a given status

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

#4317 - Fix missing genes, links and functional anno for fusion variants in causatives and verified pages

Pull Request - State: closed - Opened by northwestwitch 9 months ago - 2 comments
Labels: Bugfix

#4316 - Fixes needed before implementing orpha codes

Pull Request - State: closed - Opened by TereseBo 10 months ago - 3 comments

#4315 - Add REVEL, REVEL rank and SpliceAI scores to causatives and validated pages

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 2 comments

#4314 - Round CADD score values on causatives page

Issue - State: closed - Opened by northwestwitch 10 months ago

#4312 - Fixed missing cryptography lib error with Docker on ARM processor

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 3 comments
Labels: Easy, QualityOfLife

#4311 - Add SpliceAI-values and REVEL scores to causatives page

Issue - State: closed - Opened by northwestwitch 10 months ago
Labels: enhancement, Customer Request

#4310 - Fix missing phenomodels icon

Pull Request - State: closed - Opened by northwestwitch 10 months ago - 3 comments
Labels: Easy, Bugfix