Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / Clinical-Genomics/cg issues and pull requests

#2584 - Extract database initialisation

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

#2583 - PDC search pattern not catching all flow cells

Issue - State: closed - Opened by Vince-janv about 1 year ago
Labels: Bug, Gain L, Effort M, Urgency L, production

#2582 - Invalid sample ids on sample sheet

Issue - State: closed - Opened by seallard about 1 year ago - 1 comment
Labels: Bug, Effort M, Urgency L

#2581 - String coercion for all scout models

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

#2580 - bug(Fluffy cases are started without all fastq files

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

#2579 - Migrate delivery report models to Pydantic v2

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

#2578 - Fix deprecated import warnings

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

#2577 - Add string coercion for parent

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

#2576 - Ensure Alembic upgrades work in production

Issue - State: open - Opened by islean about 1 year ago - 1 comment
Labels: Bug

#2575 - BCLConvert and SPRING compress files to different levels

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

#2574 - Lock flask

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

#2573 - Revert "Add lab_contact to Customer"

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

#2572 - Order portal broken

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

#2571 - Lock genologics package

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

#2570 - Fix ScoutExportCase string coercion

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

#2569 - Error in cleaning old BAMs

Issue - State: closed - Opened by henrikstranneheim about 1 year ago - 4 comments
Labels: Bug

#2568 - Upgrade to Python 3.11

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

#2567 - Align cases selected for start-available

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

#2566 - Upgrade to Python 3.10

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

#2565 - Upgrade to Python 3.9

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

#2564 - RNA alignment files for Scout upload

Issue - State: open - Opened by dnil about 1 year ago - 1 comment
Labels: Scout

#2563 - Use new cg specific environments

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

#2562 - Add flow cell id to path of spring, fastq and metadata files

Issue - State: closed - Opened by diitaz93 about 1 year ago - 11 comments

#2561 - fix(covid order) Fix header to match the currently used excel sheet

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

#2560 - Add lab_contact to Customer

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

#2559 - Sort all imports

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

#2557 - Upgrade Python to 3.8

Pull Request - State: closed - Opened by seallard about 1 year ago - 13 comments

#2556 - Upgrade core packages

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

#2555 - refactor(FlowCellDirectoryData part 1)

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

#2554 - Avoid stale connections

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

#2553 - Fix deprecation warnings

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

#2552 - feat(ordeform 1508) Support new orderform version

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

#2551 - Catch sample sheet missing exception

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

#2549 - Move housekeeper functions into hk api module

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

#2548 - Update flow cells in statusDB for samples with unknown flow cell

Issue - State: closed - Opened by diitaz93 about 1 year ago - 10 comments

#2547 - Removal of mismatched spring metadata files

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

#2546 - Add read threshold for rnafusion

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

#2545 - RNAfusion cases starting regardless of reaching ordered reads

Issue - State: closed - Opened by SofiaOtero about 1 year ago
Labels: Bug, Gain L, Effort M, Urgency M, rnafusion

#2544 - Hide logic for retrieving latest sample sheet

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

#2543 - Remove unnecessary wrapper function

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

#2542 - Change float comparsion

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

#2541 - Re-implement DeleteDemuxAPI

Issue - State: open - Opened by Vince-janv about 1 year ago - 2 comments
Labels: Gain L, Effort S, Urgency M

#2540 - refactor(FlowCellDirectoryData)

Pull Request - State: closed - Opened by ChrOertlin about 1 year ago - 17 comments

#2539 - fix(code smell)

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

#2538 - Remove duplicate to_dict

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

#2537 - Add tests for the validators for ExcelSample

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

#2535 - Add flow cell id as a tag of decompressed spring files and their metadata

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

#2534 - Curate the database of inaccurate data.

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

#2533 - Add application limitations table

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

#2532 - Set reads_updated_at when reads are updated

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

#2531 - Update to Pydantic v2 in meta/upload/scout

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

#2530 - Decompress spring files to know their flow cell

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

#2529 - feat(clean flow cells)

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

#2528 - Add validators to sample id

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

#2527 - Refactor flow cell SQL filter function

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

#2526 - Encrypt flow cell 2

Pull Request - State: closed - Opened by henrikstranneheim about 1 year ago - 6 comments
Labels: Project Task

#2525 - Determine sample type from sheet content

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

#2524 - fix(sars-cov2 excel order) Properly parse the primer field

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

#2523 - Update order report templates to reads_updated_at

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

#2522 - Fix validator decorators in CGDeliverables

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

#2521 - Remove function for retrieving sample ids

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

#2520 - Delivery report missing Sekvenserad field

Issue - State: closed - Opened by ivadym about 1 year ago - 3 comments
Labels: Bug, Effort S, Urgency L

#2519 - Fix complicated comparison code smell

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

#2518 - Remove cg dependency from cgmodels

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

#2517 - feat(encryption)

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

#2516 - delete(clean flow cells cli)

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

#2515 - Hotfix for flow cell error

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

#2514 - Deprecate `archived_sample_sheet`

Issue - State: closed - Opened by diitaz93 about 1 year ago - 3 comments
Labels: demultiplex

#2513 - Tag existing Spring files with their flow cell id.

Issue - State: closed - Opened by islean about 1 year ago - 17 comments

#2512 - feat(dragen): Use cg-dragen2

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

#2511 - fix(FASTQ-upload) Prevent all FASTQ uploads from failing if one fails

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

#2510 - Add has backup flowcell

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

#2509 - fix(demultiplexing post-processing) Set flow cell status to ondisk

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

#2508 - fix(gisaid-upload) Change validator structure for GisaidSample

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

#2507 - Add has_backup to flow cell table in StatusDB

Issue - State: closed - Opened by henrikstranneheim about 1 year ago - 4 comments
Labels: Urgency L, Project Task

#2506 - Refactor encryption dir in config

Pull Request - State: closed - Opened by henrikstranneheim about 1 year ago - 12 comments
Labels: Project Task

#2505 - Remove strict qc controls for uploading microsalt cases to HK

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

#2504 - standardise the bcl2fastq demultiplexing

Issue - State: closed - Opened by ChrOertlin about 1 year ago - 5 comments
Labels: Needs Refinement, demultiplex

#2503 - clean API requires refactoring

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

#2502 - refactor(clean config)

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

#2501 - RNAFUSION: update filenames for 2.4.0

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

#2500 - Microsalt cases are not storing

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

#2499 - Upgrade sqlalchemy to 1.4

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

#2498 - Validating lsyncd transfer not functioning

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

#2497 - Migrate SQLAlchemy from 1.3 to 2.0

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

#2496 - Remove alchy from requirements

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

#2495 - Add sample_id for already created FASTQ files

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

#2494 - Store undetermined fastqs and metrics for non pooled samples

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

#2493 - fix(write sample id to sample name in bcl2fastq sample sheet)

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

#2492 - Demultiplexing flow using bcl2fastq requires adjustments

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

#2491 - Patch sample sheet sample id property

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

#2490 - Fix alembic script

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

#2489 - Revert "Sync cg and statusDB"

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

#2488 - feat(cg downsample)

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

#2487 - Encrypt flow cell

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

#2486 - Archive flow cell - WIP

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

#2485 - 2419 hook up metrics for undetermined

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