Clinical-Genomics/cg issues and pull requests

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

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

#2339 - Fix validator for rnafusion

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

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

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

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

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

#2336 - Add command for copying demultiplexed novaseqx flow cell

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

#2335 - Repeating fixtures

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

#2334 - refactor common code lines between rnafusion and taxprofiler

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

#2333 - Missing APIs in config

Issue - State: open - Opened by ChrOertlin over 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 over 1 year ago - 3 comments

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

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

#2329 - refactor(demultiplexing api)

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

#2328 - feat(dynamic setting of bcl converter)

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

#2327 - Move demultiplexing of hiseqx and hiseq2500 to cg

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

#2325 - Refactor sample sheet methods

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

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

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

#2323 - Fix existence check for sample on flow cell

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

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

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

#2321 - added command to decrypt, added process test

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

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

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

#2319 - (Archiving) get job status

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

#2318 - refactor get parameters from model

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

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

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

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

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

#2315 - Remove old demux post processing flow from cli

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

#2313 - Refactor token validation

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

#2312 - (Archiving) archive all spring files

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

#2311 - refactor(gsaidAPI)

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

#2309 - refactor(NfHandler) replace TowerAnalysisAPI and NextflowAnalysisAPI

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

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

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

#2307 - Archiving make spring archive api agnostic

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

#2305 - delete(cgstats)

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

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

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

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

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

#2301 - Delete old demux post processing workflow

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

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

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

#2298 - Create parent models for archiving

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

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

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

#2296 - patch(requirements) update housekeeper version requirement

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

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

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

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

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

#2291 - Rename trailblazer api variables

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

#2290 - Rename trailblazer api class to client

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

#2289 - fix(rnafusion): validate sample sheet

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

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

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

#2287 - delete(old demux post processing workflow)

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

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

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

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

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

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

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

#2281 - Fix sample fastq name validation

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

#2280 - Fix fastq file pattern bug

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

#2278 - Add `cg downsample` subcommand

Issue - State: closed - Opened by fevac over 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 over 1 year ago - 2 comments

#2275 - refactor(demux post processing api)

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

#2274 - Return if flow cell is not valid

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

#2273 - Add check whether flow cell should be finished

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

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

Pull Request - State: closed - Opened by Vince-janv over 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 over 1 year ago - 3 comments
Labels: Project Task

#2268 - Add endpoint for retrieving sequencing metrics

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

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

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

#2266 - temporary bump of pydantic to 2.0.3

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

#2264 - refactor FlowCellDirectoryData.id attribute

Issue - State: open - Opened by ChrOertlin over 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 over 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 over 1 year ago - 1 comment

#2261 - refactor(remove duplicated attribute)

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

#2260 - #2246: Fix copying of sample sheet

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

#2259 - refactor - move fixtures out of conftest

Pull Request - State: open - Opened by diitaz93 over 1 year ago - 1 comment
Labels: Needs Refinement, Refactor

#2258 - add(track demux logs in housekeeper)

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

#2257 - feat(copy sample sheet demux post processing new)

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

#2256 - feat(delivery-report): Upload forced generated report

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

#2255 - change(rnafusion): allow qc and complete TB status when storing

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

#2254 - enhance(set rsync api production QOS to high)

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

#2253 - refactor(tests using sql alchemy functions)

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

#2252 - add(constant for novaseqx q30 threshold)

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

#2249 - Update to Pydantic v2

Issue - State: closed - Opened by islean over 1 year ago - 1 comment
Labels: backend

#2248 - fix(sample column dependence for when parsing sample internal ids from sample sheets)

Pull Request - State: closed - Opened by ChrOertlin over 1 year ago - 5 comments

#2245 - Require Pydantic v1

Pull Request - State: closed - Opened by islean over 1 year ago - 1 comment

#2244 - feat(add extraction of sample internal ids from sample sheet to sample sheet logic)

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

#2243 - Changed Black version to be compatible with Python 3.7

Pull Request - State: closed - Opened by islean over 1 year ago - 1 comment

#2240 - Draft(archiving) Add an API that can handle archiving of samples

Pull Request - State: closed - Opened by Vince-janv over 1 year ago - 4 comments

#2239 - add(novaseqx support flow cell model statusdb)

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

#2237 - Refactor transfer of fastq files in new post processing of flow cells

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

#2236 - Add integration test for post processing of flat flow cell demultiplexed with bclconvert

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

#2235 - Add integration test for post processing of flow cell demultiplexed with bcl2fastq

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

#2233 - Added summary log and removed unnecessary check

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

#2232 - feat(Balsamic): upload of SVs to Scout for UMI cases

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

#2231 - (feat taxprofiler) Add sample_name instead of case_id in the samplesheet

Pull Request - State: closed - Opened by sofstam over 1 year ago - 4 comments
Labels: cg, Project Task, taxprofiler

#2230 - #2056: Move fixtures to root conftest

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

#2229 - Remove parsing of RunInfo from new bcl convert parserr

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

#2228 - Add is_clinical to table Customer

Pull Request - State: closed - Opened by islean over 1 year ago - 4 comments

#2227 - add(novaseqx demux post processing)

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

#2226 - Fetch sample sheet from housekeeper if available - renaming of existing files?

Issue - State: closed - Opened by karlnyr over 1 year ago
Labels: Gain S, Effort M, Urgency S, Needs Refinement

#2224 - Add integration test for post processing of flow cell demultiplexed with bclconvert

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

#2222 - change(delivery-report): Cancer panel bed extraction

Pull Request - State: closed - Opened by ivadym over 1 year ago - 3 comments

#2220 - Remove dummy samples from sample sheets

Pull Request - State: open - Opened by seallard over 1 year ago - 10 comments

#2219 - Missing limitations in RNAFUSION delivery report

Issue - State: closed - Opened by fevac over 1 year ago - 6 comments
Labels: rnafusion

#2218 - fix(decouple nipt upload from cgstats)

Pull Request - State: closed - Opened by ChrOertlin over 1 year ago - 5 comments

#2216 - Remove index checks from sample sheets

Issue - State: closed - Opened by seallard over 1 year ago
Labels: Gain L, Effort M, Urgency S

GitHub / Clinical-Genomics/cg issues and pull requests