Clinical-Genomics/cg issues and pull requests

#2484 - Create metrics for non pooled undetermined reads from bclconvert

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

#2483 - Patch fluffy sample sheet header

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

#2482 - Add conditional to override cycles checking if is_reverse_complement

Pull Request - State: closed - Opened by diitaz93 about 1 year ago - 4 comments

#2481 - feat(ruff): Update

Pull Request - State: closed - Opened by henrikstranneheim about 1 year ago - 2 comments
Labels: Enhancement

#2480 - Create metrics for non pooled undetermined reads from bcl2fastq

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

#2479 - Replace deprecated parse_file

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

#2478 - feat(isort): Add

Pull Request - State: closed - Opened by henrikstranneheim about 1 year ago - 2 comments
Labels: Enhancement

#2477 - Remove index checks

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

#2475 - Pass tags from fastq to spring upon compression

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

#2474 - Added sample id to the tags of fastq files

Pull Request - State: closed - Opened by diitaz93 about 1 year ago - 4 comments

#2473 - Pass tags from spring to fastq upon decompression

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

#2472 - cg backup retrieve CLI command not working

Issue - State: open - Opened by Vince-janv about 1 year ago - 3 comments
Labels: Bug, Gain L, Effort L, Urgency L, Needs Refinement

#2465 - Always format the fluffy sample sheet the same way

Issue - State: closed - Opened by seallard about 1 year ago

#2462 - Sync cg and statusDB

Pull Request - State: closed - Opened by islean about 1 year ago - 20 comments

#2461 - delete(cgstats)

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

#2460 - Remove unused sample sheet sample fields

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

#2459 - Unused fields on sample sheet sample types

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

#2458 - #2456: Fix fluffy config generation wip

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

#2457 - Fix(Logging) Reduce log level for error raised by is_flow_cell_ready_for_postprocessing

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

#2456 - Broken fluffly CLI command

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

#2455 - delete(TransferFlowcell class)

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

#2454 - sample sheet - override cycles, barcode mismatches and hamming distance fixes

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

#2453 - Revert order sample model migration

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

#2452 - Fix Priority parsing for RML orderform

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

#2451 - refactor(remove constructor typehints)

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

#2450 - Add software and software version used for demultiplexing

Issue - State: open - Opened by karlnyr about 1 year ago - 2 comments
Labels: Gain L, Effort M, Urgency L, Needs Refinement

#2449 - Incorrect hamming distance calculation and missing OverRideCycles

Issue - State: open - Opened by karlnyr about 1 year ago - 1 comment
Labels: Bug, Gain L, Effort M, Urgency L

#2448 - Refactor sample sheet property

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

#2447 - Balsamic v13 release changes

Issue - State: open - Opened by ivadym about 1 year ago
Labels: Balsamic

#2446 - Refactor samplesheet prop

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

#2445 - Refactor logic for retrieving sample ids from sample sheet

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

#2444 - Remove fixture pytest and name args decorator

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

#2443 - change section to bclconvert

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

#2442 - Fix create content of sample sheet for novaseq6000

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

#2441 - patch(Excel parsing) Replace spaces with underscores for priority

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

#2440 - Migrate lims models to Pydantic v2

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

#2439 - Migrate demux sample

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

#2438 - Migrate sbatch to Pydantic v2

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

#2437 - Remove verbose doc strings

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

#2436 - Move store functions

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

#2435 - Move file existence check into hk api

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

#2434 - Move retrieval of sample sheets into housekeeper api

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

#2433 - Fix validate sample fastq files for a less strict check

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

#2432 - Fix(bcl2fastq) Add new location bcl2fastq stats file

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

#2431 - Fix validate samples for finishing flow cell

Issue - State: open - Opened by diitaz93 about 1 year ago

#2430 - Changing demux path for novaseq6000 flow cells requires samplesheet manipulation for previously demultiplexed flow cells

Issue - State: closed - Opened by ChrOertlin about 1 year ago - 4 comments
Labels: Needs Refinement

#2429 - Remove call to function blocking finishing flow cells

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

#2428 - Migrate demux results

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

#2427 - Add undetermined fastqs

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

#2426 - change path of demultiplexing output

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

#2425 - Remove unused fixtures

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

#2424 - Add start_available command

Pull Request - State: closed - Opened by sofstam about 1 year ago - 5 comments
Labels: cg, taxprofiler

#2423 - Refactor bclconvert models

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

#2422 - Refactor bcl2fastq models

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

#2421 - Migrate metrics models

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

#2419 - Addition of Undetermined FASTQs to non-pooled samples

Issue - State: closed - Opened by Vince-janv about 1 year ago - 9 comments
Labels: Bug, Effort M, Urgency L, Needs Refinement

#2418 - Revert "Migrate sample sheet models to Pydantic v2 (#2394)(patch)"

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

#2417 - Migrate wip

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

#2416 - Migrate tax profiler models

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

#2415 - Should field be optional on data delivery config

Issue - State: closed - Opened by seallard about 1 year ago - 2 comments
Labels: Needs Refinement

#2414 - Change sample.sequenced_at to reads_updated_at

Pull Request - State: closed - Opened by islean about 1 year ago - 8 comments

#2413 - Start adding start command

Pull Request - State: closed - Opened by sofstam about 1 year ago - 5 comments
Labels: cg, taxprofiler

#2412 - Migrate cg config models to Pydantic v2

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

#2411 - Migrate scout tags

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

#2410 - Migrate gisaid models

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

#2409 - Migrate archive

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

#2408 - Add coercion to string for age_at_sampling

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

#2407 - Rnafusion cli options cleanup

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

#2406 - Migrate nipt models

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

#2405 - Migrate mutant sample config model

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

#2404 - Migrate slurm model

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

#2403 - feat(NovaSeq X) Parse manifest file to ensure sync

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

#2402 - Add support for tsv files to the csv module

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

#2401 - Check if fastq files exist for a sample before adding

Pull Request - State: closed - Opened by diitaz93 about 1 year ago - 4 comments
Labels: Project Task

#2400 - Pydantic validation of age_at_sampling in OrderSample

Issue - State: closed - Opened by diitaz93 about 1 year ago - 1 comment
Labels: Effort S, backend

#2399 - Fix volume type

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

#2398 - Migrate scout models

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

#2397 - Patch analysis type

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

#2396 - Make sure the flow cell retrieved from PDC is the latest version

Issue - State: open - Opened by Vince-janv about 1 year ago - 1 comment
Labels: Bug, Gain S, Effort S

#2395 - fix(post processing flow - dont add sample lane metrics if we dont have fastq files)

Issue - State: closed - Opened by karlnyr about 1 year ago - 5 comments
Labels: Bug, Gain M, Effort S, Urgency S

#2394 - Migrate sample sheet models

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

#2393 - fix(correct path to novaseqx fastq files)

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

#2392 - Migrate index model

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

#2391 - Rename NextflowSample class and children

Issue - State: closed - Opened by fevac about 1 year ago - 2 comments
Labels: rnafusion

#2390 - Migrate SampleData model

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

#2389 - fix(add abort check)

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

#2388 - Set correct sequenced_at when using new finish flow cell commands

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

#2387 - fix(overlooked code smell)

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

#2386 - feat(move to new demux flow)

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

#2385 - Add new sequencing step info for the NovaSeq X in LIMS

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

#2384 - fix(rename fastq files in new demux post processing flow)

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

#2383 - Refactor sample sheet handling in FlowCellDirectoryData

Issue - State: open - Opened by Vince-janv about 1 year ago
Labels: Gain M, Effort S, Urgency M, demultiplex

#2382 - feat(demultiplexing) Add check for demultiplexing on on-deck dragen

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

#2381 - fix(fetch HK sample sheet for validation new demux post processing flow)

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

#2380 - delete(old post processing flow)

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

#2379 - Migrate trailblazer pydantic models

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

#2378 - feat(workflow start) Simplify case availability checks

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

#2377 - Remove unused metrics field

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

#2376 - Migrate crunchy models

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

#2375 - fix(bcl converter fetching for demux post postprocessing api)

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

GitHub / Clinical-Genomics/cg issues and pull requests