Ecosyste.ms: Issues

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GitHub / Clinical-Genomics/scout issues and pull requests

#4518 - Add link chanjo2 coverage report on gene panel page

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 4 comments
Labels: enhancement, Easy

#4517 - Store demo case file paths as absolute paths

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 12 comments

#4516 - Provide a test for the chanjo2_coverage_report endpoint

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 2 comments
Labels: Easy

#4515 - plugin for variant export

Issue - State: closed - Opened by parlar 7 months ago - 3 comments
Labels: question

#4514 - More API pin fix

Pull Request - State: closed - Opened by dnil 7 months ago - 3 comments

#4513 - pin/unpin on api with document id only can't make event link now...

Issue - State: closed - Opened by dnil 7 months ago
Labels: bug

#4512 - Add link to chanjo2 coverage on gene panel page

Issue - State: closed - Opened by northwestwitch 7 months ago
Labels: enhancement

#4511 - Support for local (private?) IGV tracks

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 5 comments

#4510 - Filtering by 'Qual' on cancer variants page

Issue - State: open - Opened by cogrho 7 months ago - 5 comments
Labels: enhancement

#4509 - Support for local IGV tracks

Issue - State: closed - Opened by northwestwitch 7 months ago
Labels: enhancement

#4508 - Fix search for variants in genes present only in build 38 returning no results

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 3 comments
Labels: Easy, Bugfix

#4507 - Fusion specific fields missing from variantS export

Issue - State: closed - Opened by dnil 7 months ago
Labels: enhancement

#4506 - hg38 only genes not searchable, at least on fusion page?

Issue - State: closed - Opened by dnil 7 months ago - 1 comment
Labels: bug

#4505 - Loading HGNC gene group loci

Issue - State: closed - Opened by dnil 7 months ago
Labels: enhancement, Intermediate

#4504 - Redirect on login seems erratic

Issue - State: open - Opened by dnil 7 months ago
Labels: QualityOfLife

#4503 - Parse genes partial fusion pairs

Pull Request - State: closed - Opened by dnil 7 months ago - 8 comments

#4502 - Apply dark mode styling to multi selects rendered by select2

Pull Request - State: closed - Opened by TereseBo 7 months ago - 3 comments

#4501 - Internal disease links in disease table on diagnosis page now opens in new tab

Pull Request - State: closed - Opened by TereseBo 7 months ago - 5 comments

#4500 - Add accordion to comment box

Pull Request - State: closed - Opened by TereseBo 7 months ago - 3 comments

#4499 - Version 4.79.1 - patch export variants without rankscore

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

#4498 - Fix bug exporting variants without rank score

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 2 comments
Labels: Easy, Bugfix

#4497 - Display custom annotations also on cancer variant page

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 2 comments
Labels: Easy

#4496 - Rank score key missing when exporting variants triggers crash

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

#4495 - Fix visualization of custom annotations on cancer variants pages

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

#4494 - Open link to OMIM/ORPHA from Diagnosis page on new tab

Issue - State: closed - Opened by dnil 7 months ago
Labels: Easy, Frontend

#4493 - Fix #4491 - case incidental finding tag

Pull Request - State: closed - Opened by dnil 7 months ago - 2 comments
Labels: enhancement, Easy

#4492 - Fix #4490 - route document_id var to category view

Pull Request - State: closed - Opened by dnil 7 months ago - 3 comments
Labels: Easy

#4491 - Add incidental finding case tag

Issue - State: closed - Opened by dnil 7 months ago
Labels: enhancement, Easy

#4490 - Route to variant view with document id should end up on expected view

Issue - State: closed - Opened by dnil 7 months ago
Labels: Refactor

#4488 - Minor release 4.79

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 3 comments

#4487 - Fix #4476 - links to SV classification guideline and guide.

Pull Request - State: closed - Opened by dnil 7 months ago - 2 comments
Labels: Customer Request, Easy, Frontend

#4486 - Add instructions on how to connect scout to chanjo2

Issue - State: closed - Opened by northwestwitch 7 months ago
Labels: enhancement, docs

#4485 - Amend typo in #4483

Pull Request - State: closed - Opened by dnil 7 months ago - 2 comments
Labels: Easy, Bugfix

#4484 - ACMG on report - part two

Pull Request - State: closed - Opened by dnil 7 months ago - 1 comment

#4483 - Fix #4480 - show ACMG VUS on general report

Pull Request - State: closed - Opened by dnil 7 months ago - 4 comments
Labels: Easy, Bugfix

#4482 - 'Institutes to share cases with' select displays institute names and IDs

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 3 comments
Labels: Customer Request, Easy

#4481 - [obophenotype/human-phenotype-ontology] Release v2024-03-06 - 2024-03-06 Release

Issue - State: closed - Opened by dnil 7 months ago - 5 comments
Labels: Task

#4480 - Other commented variant missing from somatic general report?

Issue - State: closed - Opened by dnil 7 months ago - 1 comment
Labels: bug

#4478 - Logs for obs_cases

Pull Request - State: closed - Opened by TereseBo 7 months ago - 2 comments

#4477 - Add Cust no to "Share cases"

Issue - State: closed - Opened by KickiLagerstedt 7 months ago - 2 comments
Labels: Customer Request, Easy, QualityOfLife

#4476 - Add link(s) to SV classification guidelines

Issue - State: closed - Opened by dnil 7 months ago
Labels: enhancement, Customer Request

#4475 - Reroute case no institute

Pull Request - State: closed - Opened by dnil 7 months ago - 3 comments
Labels: enhancement

#4474 - Add button for displaying STR variants occurring in the dynamic HPO panel on case page

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 6 comments
Labels: Customer Request, Easy

#4473 - Clinical HPO STRs-button

Issue - State: closed - Opened by SofieCMD 7 months ago - 1 comment
Labels: enhancement

#4472 - Fix orpha phenomodels

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

#4471 - Fix #4470 - add sniffles and cnvpytor

Pull Request - State: closed - Opened by dnil 7 months ago - 2 comments
Labels: Easy

#4470 - Add a few LRS callers

Issue - State: closed - Opened by dnil 7 months ago
Labels: enhancement, Easy

#4469 - Parse trgt VCFs for STR variants

Issue - State: closed - Opened by dnil 7 months ago - 1 comment
Labels: enhancement, LRS

#4468 - refactoring phenotype to disease

Pull Request - State: closed - Opened by TereseBo 7 months ago - 3 comments

#4467 - Replaced omim_terms where orphaterms were included

Pull Request - State: closed - Opened by TereseBo 7 months ago - 3 comments

#4466 - disease_term genes now include both symbol and id when fetched from api

Pull Request - State: closed - Opened by TereseBo 7 months ago - 3 comments

#4465 - Display common/uncommon/rare on mei variant summary

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 3 comments
Labels: Easy

#4464 - MEI summary frequency badge could be populated

Issue - State: closed - Opened by dnil 7 months ago - 2 comments
Labels: enhancement

#4463 - Show MANE functional annotations on variant's summary

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 8 comments

#4462 - Minor release 4.78

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 8 comments

#4461 - Modify variants to display MANE info from Ensembl and not VEP annotations

Pull Request - State: closed - Opened by northwestwitch 7 months ago - 16 comments

#4460 - nf-core raredisease - peddy het check

Issue - State: closed - Opened by dnil 7 months ago - 3 comments
Labels: enhancement, question, nf-core/raredisease

#4459 - Replace "omim" with "disease" in case page query search and related functions

Pull Request - State: closed - Opened by TereseBo 7 months ago - 3 comments

#4458 - bug? missing manual and omim inheritence

Issue - State: closed - Opened by Leif-glitch 7 months ago - 3 comments
Labels: question

#4457 - Add option to search disease_terms in database to diagnosis page

Pull Request - State: closed - Opened by TereseBo 7 months ago - 3 comments

#4456 - Gnomad keys

Pull Request - State: closed - Opened by dnil 8 months ago - 7 comments

#4454 - Fix #4329 - add XTR to PAR definition

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

#4453 - API - add a variant

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

#4452 - API - update manual rank

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

#4451 - Fix #4157 - add pin API endpoint

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

#4450 - Display MANE badges on gene pages

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

#4449 - Update Decipher base urls

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

#4448 - Parse and save MANE transcripts info when updating genes in build 38

Pull Request - State: closed - Opened by northwestwitch 8 months ago - 6 comments
Labels: Easy

#4447 - Malformed queries in DECIPHER links for SV variants

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

#4446 - nf-core raredisease VEP 110 parsing

Issue - State: closed - Opened by dnil 8 months ago - 6 comments
Labels: enhancement, nf-core/raredisease

#4445 - nf-core raredisease separate MT files

Issue - State: closed - Opened by dnil 8 months ago - 4 comments
Labels: enhancement, blocked, nf-core/raredisease

#4444 - Can we add more information for CNVs uploaded to Scout?

Issue - State: open - Opened by mathiasbio 8 months ago - 4 comments
Labels: enhancement, Cancer

#4443 - Fix #4442 - do not bring in ORPHA inheritance model to OMIM specific …

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

#4442 - ORPHA phenotype

Issue - State: closed - Opened by Leif-glitch 8 months ago - 5 comments
Labels: bug

#4441 - Fix #4396 - reset default loglevel to INFO

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

#4440 - Fix #4435 - add MEI element name to variant page

Pull Request - State: closed - Opened by dnil 8 months ago - 2 comments
Labels: Easy, Frontend

#4439 - Changed the cases.utils.remove button x color for better visibility

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

#4438 - Rename Clinical Significance to Germline Classification on multistep ClinVar form

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

#4437 - Fix #4436 - update GitHub Actions

Pull Request - State: closed - Opened by dnil 8 months ago - 7 comments
Labels: Easy

#4436 - Outdated actions

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

#4435 - MEI annotation "Element" should be shown on variant page

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

#4434 - Two new SO terms (`sequence_variant` and `coding_transcript_variant`)

Pull Request - State: closed - Opened by alkc 8 months ago - 6 comments

#4433 - Keep beacon and Matchmaker status for reuploaded cases

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

#4432 - Matchmaker submission data gets erased on case rerun

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

#4431 - Show the CSQ/Function of related MANE transcript in gene summary in variant view

Issue - State: closed - Opened by alkc 8 months ago - 2 comments
Labels: enhancement

#4430 - Rename Clinical significance to Germline classification

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

#4429 - Remove diagnosis X a bit hard to find..

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

#4428 - ORPHA term caseS search

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

#4426 - Add option of downloading clinvar submission as .json

Pull Request - State: closed - Opened by TereseBo 8 months ago - 6 comments

#4425 - Version 4.77

Pull Request - State: closed - Opened by dnil 8 months ago - 10 comments

#4421 - Removed log to console

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

#4420 - Add clinvar assertion criteria selection

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

#4419 - Fix #4418 - report division-by-zero on depth 0

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

#4418 - ZeroDivisionError: division by zero while loading case report

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

#4417 - Missing SO terms in `scout.constants.so_terms.py`

Issue - State: closed - Opened by alkc 8 months ago - 7 comments
Labels: enhancement

#4416 - [obophenotype/human-phenotype-ontology] Release v2024-02-08

Issue - State: closed - Opened by dnil 8 months ago - 2 comments
Labels: Task