Clinical-Genomics/cg issues and pull requests

#2684 - Increase case id range

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

#2683 - Fix(Sample sheet) Granulate logic for indices

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

#2682 - Fix(tests) Improve panel pytest

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

#2681 - Older NoveSeq 6000 runs not demultiplexed properly

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

#2680 - Failing orders are partially added to databases

Issue - State: open - Opened by Vince-janv about 1 year ago - 6 comments
Labels: Needs Refinement

#2679 - Dsmc fails wih exit code 12 when backing-up flow cell encryption key

Issue - State: closed - Opened by henrikstranneheim about 1 year ago - 2 comments
Labels: Bug

#2678 - fix(move error handling clean flow cells)

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

#2677 - fix(relax clean flow cell criteria)

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

#2676 - External samples have no reads on the sample Model and are therefore not delivered properly

Issue - State: closed - Opened by Vince-janv about 1 year ago

#2675 - fix(relax clean flow cells criteria)

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

#2674 - (Archiving) Retrieve files from DDN in start command

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

#2673 - Add a new application limitation for MIP-dna and EXO in the apptag

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

#2672 - Convert to f-strings

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

#2671 - Customers cannot order re-delivery of previously existing cases

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

#2670 - Rename family in db

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

#2669 - Rename family sample

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

#2668 - Testing ruff fix

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

#2667 - Fix code smell flagged by sonarcloud

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

#2666 - Rename family relationships

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

#2665 - Remove lambda expressions

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

#2664 - Add qc check to mutant before storing

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

#2663 - Patch view

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

#2662 - Update patched package versions

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

#2661 - Add Rnafusion alignment file to Scout uploads

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

#2660 - Set reads_updated_at to sequencing date

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

#2659 - Retrieve undetermined fastqs in root for flow cells with flat output

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

#2658 - Unwanted analyses starting after re-demultiplexing of old flow cells

Issue - State: closed - Opened by Vince-janv about 1 year ago - 6 comments
Labels: Bug

#2657 - Update Balsamic API (Balsamic v13 release)

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

#2656 - Fix toml

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

#2655 - Rename Family to Case

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

#2654 - Event driven architecture

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

#2653 - feat - add HiSeq RunParameters file parser

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

#2652 - Add Mutant QC

Issue - State: closed - Opened by karlnyr about 1 year ago - 6 comments
Labels: Good first issue, Gain S, Effort M, Urgency S

#2651 - Extract index and read length from RunParameters of HiSeq flow cells

Issue - State: closed - Opened by diitaz93 about 1 year ago - 1 comment
Labels: Needs Refinement, demultiplex

#2650 - fix: rename sampleID in scout.yaml for balsamic

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

#2649 - add raredisease to cli cg workflow

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

#2648 - feat(tb): Remove unused function

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

#2647 - Reads Updated At behaviour

Issue - State: closed - Opened by fevac about 1 year ago - 1 comment
Labels: Needs Refinement

#2646 - Revert "feat(raredisease): Add raredisease to cg workflow"

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

#2645 - Replace hardcoded validation cases

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

#2644 - chore: Create add-to-bl.yml

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

#2643 - Refactor workflow tests for the nextflow pipelines

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

#2642 - Fix database model error

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

#2641 - Missed pending decompression check

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

#2640 - Bump werkzeug from 3.0.0 to 3.0.1

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 3 comments
Labels: dependencies

#2639 - Bump urllib3 from 2.0.6 to 2.0.7

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 3 comments
Labels: dependencies

#2638 - patch(PDC fetching) Except warnings from the dsmc command

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

#2637 - Remove cascade backrefs parameter

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

#2636 - Fix enums

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

#2635 - Ensure connection is closed after CLI commands

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

#2634 - Populate sample concentration thresholds

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

#2633 - Containerizing the cg CLI

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

#2632 - Add GENS upload command for BALSAMIC cases

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

#2631 - Add application details to delivery report

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

#2630 - Ambiguous housekeeper tags for GENS upload

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

#2629 - Add sample_concentration min/max

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

#2628 - Add poetry

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

#2627 - Delivery report key existence check at time of upload

Issue - State: open - Opened by pbiology about 1 year ago - 7 comments

#2626 - Sample concentration is given as a string

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

#2625 - Fix rnafusion analysis version

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

#2624 - Set delivery files as optional for rnafusion

Pull Request - State: closed - Opened by fevac about 1 year ago - 11 comments
Labels: rnafusion

#2623 - feat(Data transfer) Create manifest file in flow cell directories

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

#2622 - Add pipeline limitations endpoint

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

#2621 - Update Rnafusion for release v3.0.1

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

#2620 - Analysis version pipeline changed for rnafusion

Issue - State: closed - Opened by fevac about 1 year ago
Labels: Bug, rnafusion

#2619 - fix(demultiplexing )Remove demux dir before starting a new demux job

Pull Request - State: closed - Opened by Vince-janv about 1 year ago - 4 comments
Labels: demultiplex

#2618 - Broken priority value presented in Susy order summaries

Issue - State: closed - Opened by Karl-Svard about 1 year ago
Labels: Bug, Gain M, Effort S, production

#2617 - Fix warnings in tests

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

#2616 - Add pipeline limitations to delivery report

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

#2615 - Upgrade SQLAlchemy to 2.0

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

#2614 - Fix relationship copy warning

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

#2613 - Set future flag on session

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

#2612 - Reflect changes in housekeeper in the hk module

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

#2611 - Use future flag on engine

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

#2610 - Containerize cg cli

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

#2609 - Fix missed session warnings

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

#2608 - Missed is_flow_cell_check_applicable

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

#2607 - Remove hard coded validation cases

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

#2606 - Update validation cases

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

#2605 - Patch errors

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

#2604 - Remove archived sample sheet tag and logic

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

#2603 - Add delivery of analysis for microSALT

Issue - State: open - Opened by talnor about 1 year ago - 1 comment

#2602 - Updated pydantic version req

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

#2601 - Fix join

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

#2600 - Fix missed join

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

#2599 - Remove logic regarding archived sample sheet

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

#2598 - Fix session merge warnings

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

#2597 - Fix code smell by refactoring add_decompressed_fastq_files_to_housekeeper

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

#2596 - Extract database module

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

#2595 - Add customer lab contact

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

#2594 - Lock broken lib

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

#2593 - Delete old flow cell before adding re-demultiplexed flow cell

Pull Request - State: closed - Opened by diitaz93 about 1 year ago - 8 comments

#2592 - feat(raredisease): Add raredisease to cg workflow

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

#2591 - Replace csrf protection lib

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

#2590 - add raredisease to constants

Pull Request - State: closed - Opened by peterpru about 1 year ago - 1 comment
Labels: cg, raredisease

#2589 - Fix deprecated joins warnings

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

#2588 - fix(Flow cell Retrieval) Fix search pattern to find all flow cells

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

#2587 - Refactor to pep 0585

Pull Request - State: closed - Opened by henrikstranneheim about 1 year ago - 3 comments
Labels: Enhancement

#2586 - Add backup flow cells

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

#2585 - Fix deploy in template

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

GitHub / Clinical-Genomics/cg issues and pull requests