Clinical-Genomics/cg issues and pull requests

#2374 - fix(sonarcloud) Removed unreachable code.

Pull Request - State: closed - Opened by Vince-janv about 1 year ago - 1 comment

#2373 - Hotfix for setting sequenced at in temp finish

Pull Request - State: closed - Opened by islean about 1 year ago - 3 comments

#2372 - Remove bcl converter from parameters finish commands

Pull Request - State: closed - Opened by diitaz93 about 1 year ago - 3 comments

#2371 - Add exception catching for demultiplex finish-all commands

Pull Request - State: closed - Opened by diitaz93 about 1 year ago - 2 comments

#2370 - Updates to pydantic v2 in sequencing_metrics_parser

Pull Request - State: closed - Opened by islean about 1 year ago - 2 comments

#2369 - Refine the start demultiplexing command of NovaSeqX flow cells

Issue - State: closed - Opened by karlnyr about 1 year ago - 4 comments
Labels: Gain L, Effort S, Urgency L

#2368 - The automation tries (and fails) to start a demultiplex process of NovaSeq X flow cells after copying is complete

Issue - State: closed - Opened by Karl-Svard about 1 year ago - 6 comments

#2367 - refactor(nf_analysis) deliverables as model

Pull Request - State: open - Opened by fevac about 1 year ago - 1 comment

#2366 - Update to pydantic v2 in apps/scout

Pull Request - State: closed - Opened by islean about 1 year ago - 7 comments

#2365 - Added expected header structure in sample sheet validation

Pull Request - State: closed - Opened by islean about 1 year ago - 5 comments
Labels: Enhancement

#2364 - Patch path to sample sheet in hk

Pull Request - State: closed - Opened by diitaz93 about 1 year ago - 3 comments
Labels: Needs Refinement

#2363 - #2362: Patch new flow cell dir structure

Pull Request - State: closed - Opened by seallard about 1 year ago - 4 comments

#2362 - Finding fastq files patterns for BCLConvert pattern without the moving of files

Issue - State: closed - Opened by karlnyr about 1 year ago - 4 comments

#2361 - 2500 flowcells are not demultiplexed with the new automation

Issue - State: open - Opened by beatrizsavinhas about 1 year ago - 4 comments
Labels: demultiplex

#2360 - Refactor(rnafusion) sample sheet methods

Pull Request - State: closed - Opened by fevac about 1 year ago - 4 comments

#2359 - cg decompress doesn't include decompressed files in housekeeper

Issue - State: open - Opened by beatrizsavinhas about 1 year ago

#2358 - Update to pydantic v2 in apps/orderform

Pull Request - State: closed - Opened by islean about 1 year ago - 3 comments

#2357 - Add tower to cg workflow taxprofiler run

Pull Request - State: closed - Opened by sofstam about 1 year ago - 7 comments
Labels: cg, taxprofiler

#2356 - patch(Flask Admin view) Fix Set Action functionality

Pull Request - State: closed - Opened by Vince-janv about 1 year ago - 1 comment

#2355 - Replace taxprofiler_case_id, rnafusion_case_id with case_id

Pull Request - State: open - Opened by sofstam about 1 year ago - 1 comment

#2354 - fix - DemuxResults call in cg demultiplex report

Issue - State: closed - Opened by diitaz93 about 1 year ago - 1 comment
Labels: Bug, cg

#2353 - Update CODEOWNERS

Pull Request - State: closed - Opened by pbiology about 1 year ago - 1 comment

#2352 - Patch q30 metrics

Pull Request - State: closed - Opened by seallard about 1 year ago - 5 comments

#2351 - Update pydantic in apps/hermes

Pull Request - State: closed - Opened by islean about 1 year ago - 2 comments

#2350 - Inconsistent values for q30 metrics

Issue - State: closed - Opened by seallard about 1 year ago - 9 comments
Labels: Project Task, backend

#2349 - add(flat flow cell directory structure demux api)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 4 comments

#2348 - remove(unused test folder)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 2 comments

#2347 - 2336 copy novaseqx flowcell

Pull Request - State: closed - Opened by seallard about 1 year ago - 3 comments

#2346 - (fix) Update to pydantic v2 in Housekeeper.models

Pull Request - State: closed - Opened by islean about 1 year ago - 3 comments

#2345 - (Archiving) CLI functionality

Pull Request - State: closed - Opened by islean about 1 year ago - 9 comments

#2344 - refactor(BackupAPI use flat flow cell structure)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 3 comments

#2343 - Add sample sheet to housekeeper right after creation

Pull Request - State: closed - Opened by diitaz93 about 1 year ago - 13 comments
Labels: cg, Project Task, backend

#2342 - Use Flat flowcell runs structure

Issue - State: closed - Opened by ChrOertlin about 1 year ago - 2 comments
Labels: Project Task

#2341 - Keep flow cell data in a single directory

Issue - State: closed - Opened by seallard about 1 year ago - 3 comments
Labels: Needs Refinement

#2340 - add( flat flow cell struct to config)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 1 comment

#2339 - Fix validator for rnafusion

Pull Request - State: closed - Opened by fevac about 1 year ago - 2 comments
Labels: Bug

#2338 - fix(remove bcl converter option from demultiplex all)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 2 comments

#2337 - Copy/fetch sample sheet to/from housekeeper

Issue - State: closed - Opened by diitaz93 about 1 year ago
Labels: Project Task, backend

#2336 - Add command for copying demultiplexed novaseqx flow cell

Issue - State: closed - Opened by seallard about 1 year ago - 14 comments
Labels: Project Task, backend

#2335 - Repeating fixtures

Issue - State: open - Opened by sofstam about 1 year ago - 2 comments
Labels: Enhancement

#2334 - refactor common code lines between rnafusion and taxprofiler

Issue - State: open - Opened by sofstam about 1 year ago - 2 comments
Labels: rnafusion, taxprofiler, Refactor

#2333 - Missing APIs in config

Issue - State: open - Opened by ChrOertlin about 1 year ago - 1 comment
Labels: Enhancement, on hold

#2332 - Fix already included file call in MIP DNA auto upload.

Pull Request - State: closed - Opened by islean about 1 year ago - 3 comments

#2331 - sql duplicate entry error in upload-auto-mip-dna.sh

Issue - State: open - Opened by beatrizsavinhas about 1 year ago - 15 comments

#2329 - refactor(demultiplexing api)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 4 comments

#2328 - feat(dynamic setting of bcl converter)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 3 comments

#2327 - Move demultiplexing of hiseqx and hiseq2500 to cg

Issue - State: closed - Opened by ChrOertlin about 1 year ago - 2 comments

#2325 - Refactor sample sheet methods

Pull Request - State: closed - Opened by fevac about 1 year ago - 2 comments

#2324 - refactor(move finish flow cell all temp to utils)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 2 comments

#2323 - Fix existence check for sample on flow cell

Pull Request - State: closed - Opened by seallard about 1 year ago - 2 comments

#2322 - (Archiving) Retrieve file, sample or flowcell

Pull Request - State: closed - Opened by islean about 1 year ago - 6 comments

#2321 - added command to decrypt, added process test

Pull Request - State: closed - Opened by karlnyr about 1 year ago - 3 comments

#2320 - fix(add samples to flow cell if it already exists)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 2 comments

#2319 - (Archiving) get job status

Pull Request - State: closed - Opened by islean about 1 year ago - 6 comments

#2318 - refactor get parameters from model

Pull Request - State: closed - Opened by fevac about 1 year ago - 9 comments

#2317 - feat(retrieve demux run dir by flow cell type)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 2 comments

#2316 - Path to flow cell run directory incorrect in DemultiplexingAPI

Issue - State: closed - Opened by seallard about 1 year ago - 3 comments
Labels: Bug, demultiplex

#2315 - Remove old demux post processing flow from cli

Pull Request - State: closed - Opened by seallard about 1 year ago - 3 comments

#2313 - Refactor token validation

Pull Request - State: closed - Opened by seallard about 1 year ago - 7 comments

#2312 - (Archiving) archive all spring files

Pull Request - State: closed - Opened by islean about 1 year ago - 3 comments

#2311 - refactor(gsaidAPI)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 2 comments

#2309 - refactor(NfHandler) replace TowerAnalysisAPI and NextflowAnalysisAPI

Pull Request - State: closed - Opened by fevac about 1 year ago - 5 comments

#2308 - refactor(NfAnalysisAPI) avoid code duplication between rnafusion and taxprofiler

Pull Request - State: closed - Opened by sofstam about 1 year ago - 3 comments
Labels: Refactor

#2307 - Archiving make spring archive api agnostic

Pull Request - State: closed - Opened by islean about 1 year ago - 2 comments

#2305 - delete(cgstats)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 3 comments

#2303 - refactor(NfAnalysisAPI) avoid code duplication between rnafusion and taxprofiler

Pull Request - State: closed - Opened by fevac about 1 year ago - 5 comments

#2302 - feat(Archiving) Add archive model base class and functionality

Pull Request - State: closed - Opened by islean about 1 year ago - 5 comments

#2301 - Delete old demux post processing workflow

Issue - State: closed - Opened by ChrOertlin about 1 year ago - 1 comment

#2300 - feat(archiving) Use File and Sample models for archiving

Pull Request - State: closed - Opened by Vince-janv about 1 year ago - 2 comments

#2299 - fix(Archiving) Changed input and output types for archiving and retrieval functions

Pull Request - State: closed - Opened by Vince-janv about 1 year ago - 2 comments

#2298 - Create parent models for archiving

Pull Request - State: closed - Opened by Vince-janv about 1 year ago - 3 comments

#2297 - fix(Loqusdb): Cancer somatic SNV uploads

Pull Request - State: closed - Opened by ivadym about 1 year ago - 2 comments

#2296 - patch(requirements) update housekeeper version requirement

Pull Request - State: closed - Opened by Vince-janv about 1 year ago - 2 comments

#2295 - add(samples to flow cell in new demux pp workflow)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 8 comments
Labels: Project Task

#2294 - fix(uncouple statusDB Sample reads from CGstats)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 5 comments
Labels: Project Task

#2291 - Rename trailblazer api variables

Pull Request - State: closed - Opened by seallard about 1 year ago - 1 comment

#2290 - Rename trailblazer api class to client

Pull Request - State: closed - Opened by seallard about 1 year ago - 2 comments

#2289 - fix(rnafusion): validate sample sheet

Pull Request - State: closed - Opened by fevac about 1 year ago - 3 comments

#2288 - add(force flag to new demux pp flow)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 5 comments
Labels: Project Task

#2287 - delete(old demux post processing workflow)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 2 comments
Labels: Project Task

#2286 - refactor(remove cgstats from delete demux api)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 3 comments
Labels: Project Task

#2285 - Q30 values for NIPT flow cells not being calculated correctly

Issue - State: closed - Opened by Vince-janv about 1 year ago - 4 comments
Labels: Bug, Gain S, Effort S, Urgency S, Needs Refinement

#2284 - refactor(tests in demultiplex post processing)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 1 comment
Labels: Project Task

#2283 - change(rnafusion): make tower names unique when resuming

Pull Request - State: closed - Opened by fevac about 1 year ago - 3 comments

#2282 - Feat(archiving) Adds fetching and sorting functions

Pull Request - State: closed - Opened by Vince-janv about 1 year ago - 2 comments

#2281 - Fix sample fastq name validation

Pull Request - State: closed - Opened by seallard about 1 year ago - 2 comments

#2280 - Fix fastq file pattern bug

Pull Request - State: closed - Opened by seallard about 1 year ago - 3 comments

#2278 - Add `cg downsample` subcommand

Issue - State: closed - Opened by fevac about 1 year ago - 11 comments
Labels: Gain L, Effort L, Urgency M

#2276 - Avoid creating empty sample bundles

Pull Request - State: closed - Opened by seallard about 1 year ago - 2 comments

#2275 - refactor(demux post processing api)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 4 comments
Labels: Project Task

#2274 - Return if flow cell is not valid

Pull Request - State: closed - Opened by seallard about 1 year ago - 1 comment

#2273 - Add check whether flow cell should be finished

Pull Request - State: closed - Opened by seallard about 1 year ago - 2 comments

#2271 - patch(demultiplexing) Catch all error in new finish flow-cell

Pull Request - State: closed - Opened by Vince-janv about 1 year ago - 3 comments

#2269 - fix( check if sample is present in statusDB before adding a metrics entry)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 3 comments
Labels: Project Task

#2268 - Add endpoint for retrieving sequencing metrics

Pull Request - State: closed - Opened by seallard about 1 year ago - 4 comments

#2267 - Include time stamp in sequencing date for flow cells

Pull Request - State: closed - Opened by seallard about 1 year ago - 6 comments

#2266 - temporary bump of pydantic to 2.0.3

Pull Request - State: closed - Opened by diitaz93 about 1 year ago - 5 comments

#2264 - refactor FlowCellDirectoryData.id attribute

Issue - State: open - Opened by ChrOertlin about 1 year ago
Labels: Urgency S, demultiplex

#2263 - Copy sample sheet when the flow cell is created in demultiplexed-runs

Issue - State: closed - Opened by seallard about 1 year ago - 4 comments
Labels: Gain S, Effort M, Urgency S, Needs Refinement, demultiplex

#2262 - refactor(make hk log less verbose)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 1 comment

GitHub / Clinical-Genomics/cg issues and pull requests