Clinical-Genomics/cg issues and pull requests

#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

#2214 - change(Balsamic): Automatic start of normal only analyses

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

#2213 - Add data archive location to Customer table

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

#2211 - Fix Loqusdb somatic database uploads

Issue - State: closed - Opened by ivadym over 1 year ago - 5 comments
Labels: Balsamic

#2210 - Refactor RNA DNA case map to data class

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

#2209 - fix(RNAFUSION orders) Add validation for one sample per case

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

#2207 - patch(RML OF) Renamed new indexset

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

#2206 - Intermittent internal server errors for status db

Issue - State: closed - Opened by seallard over 1 year ago - 1 comment
Labels: Bug

#2205 - Roadmap for implementing automatic archiving in cg

Issue - State: open - Opened by Vince-janv over 1 year ago

#2204 - enchance(usability delete flow cell command)

Pull Request - State: closed - Opened by ChrOertlin over 1 year ago - 6 comments
Labels: Enhancement

#2203 - Fix update date in uploading MIPRNA

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

#2201 - Only store sample fastqs passing q30 in Housekeeper

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

#2193 - Add separate fields to statusDB for description and limitations for RD and cancer analyses

Issue - State: closed - Opened by ivadym over 1 year ago
Labels: Balsamic, feature

#2173 - Is it necessary to create delivery.txt in post processing of demultiplexed flow cells?

Issue - State: closed - Opened by seallard over 1 year ago - 1 comment
Labels: question, demultiplex

#2167 - Tests in module test_meta_transfer_flowcell not cleaning up

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

#2154 - Non nullable field is null in database for SampleLaneSequencingMetris

Issue - State: closed - Opened by seallard over 1 year ago - 4 comments
Labels: Bug, Gain M

#2153 - Deprecated fields on the sample model

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

#2138 - feat (SampleSheet) add barcode mismatch based on hamming distance

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

#2131 - Keep track of SPRING and FASTQ files based on flow cells

Issue - State: open - Opened by Vince-janv over 1 year ago - 7 comments
Labels: Bug, Gain L, Effort L, Urgency L

#2120 - Change variables named 'flowcell_id' to 'flow_cell_id'

Issue - State: open - Opened by diitaz93 over 1 year ago
Labels: Gain S, Effort M, Urgency S, demultiplex

#2118 - HiseqX tests using NovaSeq fixtures

Issue - State: closed - Opened by diitaz93 over 1 year ago - 2 comments
Labels: cg, backend, demultiplex

#2114 - Fetching flow cells from PDC fails

Issue - State: open - Opened by seallard over 1 year ago - 6 comments

#2110 - Remove bcl argument

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

#2106 - (feat taxprofiler): Add taxprofiler resolve-compression and run commands

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

#2098 - Sync cg with database structure

Issue - State: closed - Opened by islean over 1 year ago - 15 comments
Labels: Gain S, Effort S, Urgency S

#2081 - Non-standard session handling

Issue - State: closed - Opened by seallard over 1 year ago - 2 comments
Labels: Gain M, Effort M, Urgency M

#2080 - Fixture scopes too narrow

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

#2065 - Use data classes instead of dictionaries and tuples

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

#2063 - Fixtures that return None and perform side effects

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

#2056 - Direct imports of fixtures in tests and conftests

Issue - State: closed - Opened by seallard over 1 year ago - 5 comments
Labels: Gain M, Effort S

#2053 - Remove all unused fixtures

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

#2052 - feat(calculation bcl convert metrics)

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

#2051 - Fix Marshmallow warnings due to deprecated parameter

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

#2050 - Fix pytest warnings

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

#2049 - 1886 - duplicate /families logic to /cases

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

#2048 - Remove export command

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

#2047 - Remove status commands

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

#2046 - Fix(RNA scout config) Change dict key to be enum value

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

#2045 - Add calculation of sequencing metrics for bcl2fastq data

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

#2044 - Duplications between Rnafusion and Taxprofiler

Issue - State: open - Opened by sofstam over 1 year ago - 1 comment
Labels: Enhancement, cg, rnafusion, taxprofiler

#2043 - 2033 - single case use customer id from case instead of ticket

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

#2042 - fix(include flow cell mode S1)

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

#2041 - Remove flow cell mode

Pull Request - State: closed - Opened by diitaz93 over 1 year ago - 3 comments
Labels: Bug, cg

#2040 - Migrate verify case id in statusdb

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

#2039 - Removed housekeeper version lock

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

#2038 - Remove flow cell mode

Issue - State: closed - Opened by diitaz93 over 1 year ago - 3 comments
Labels: Gain M, cg

#2037 - feat(read csv into dict in io controller)

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

#2036 - create child classes for different sample sheet creators

Pull Request - State: open - Opened by diitaz93 over 1 year ago - 1 comment

#2035 - Rm deprecated sequncers

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

#2034 - New sample sheet v2

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

#2033 - Remove old way of dealing with tickets in the rsync step

Issue - State: closed - Opened by Vince-janv over 1 year ago - 1 comment
Labels: Bug, Good first issue

#2032 - Update author list for GISAID uploads

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

#2031 - Add module for calculating sequencing metrics

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

#2030 - Explicitly referring to DRAGEN software usage

Issue - State: open - Opened by ChrOertlin over 1 year ago - 4 comments
Labels: Good first issue, Gain S, cg, on hold

#2029 - MIP-RNA: delivery report

Issue - State: open - Opened by karlnyr over 1 year ago - 12 comments
Labels: Gain L, Effort M, Urgency L

#2028 - feat(BCL convert metric parser)

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

#2027 - Wire flow cell mode

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

#2026 - Remove version lock for werkzeug

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

#2025 - change(rnafusion) exclude files from delivery

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

#2024 - code duplication(introduce sample sheet parsing code)

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

#2023 - Fix 401 errors due to invalid certificate

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

#2022 - Add case to skip for compression

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

#2021 - add(seq_metric_parser directories)

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

#2020 - Add parser for sequencing metrics from bcl2fastq demultiplexer

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

#2019 - Use io csv with sample sheet

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

#2018 - feat(rnafusion) add clinical delivery

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

#2017 - Fix observations upload import

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

GitHub / Clinical-Genomics/cg issues and pull requests