Clinical-Genomics/cg issues and pull requests

#3582 - Patch mother in same case validation

Pull Request - State: closed - Opened by islean about 2 months ago - 1 comment

#3581 - Ensure fields are nullable

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

#3580 - (Improve order flow) Validate sex required for new samples

Pull Request - State: closed - Opened by islean about 2 months ago - 1 comment

#3579 - Add status required check

Pull Request - State: closed - Opened by islean about 2 months ago - 1 comment

#3578 - Validate existing samples do in fact exist

Pull Request - State: closed - Opened by seallard about 2 months ago - 1 comment

#3577 - (improve-order-flow) Add case internal id existence check

Pull Request - State: closed - Opened by islean about 2 months ago - 1 comment

#3576 - feat/add freshdesk properties

Pull Request - State: open - Opened by ahdamin about 2 months ago - 2 comments

#3575 - address comments from PacBio dev branch

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

#3574 - refactor(submitters)

Pull Request - State: closed - Opened by ChrOertlin about 2 months ago - 7 comments

#3573 - Validate case name is unique

Pull Request - State: closed - Opened by seallard about 2 months ago - 1 comment

#3572 - Patch unique names rules

Pull Request - State: closed - Opened by seallard about 2 months ago - 1 comment

#3571 - Add cell tag to bam file and fix tag concatenation

Pull Request - State: closed - Opened by diitaz93 about 2 months ago - 1 comment

#3570 - Rename order status column

Pull Request - State: open - Opened by islean about 2 months ago - 3 comments
Labels: alembic migration

#3569 - add(microbial fastq order submitter)

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

#3568 - Prevent GENS files being provided to Balsamic CLI for hg38

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

#3567 - Operate on new samples and cases

Pull Request - State: closed - Opened by seallard about 2 months ago - 1 comment

#3566 - Patch(clinical-delivery) Remove -p flag for rsync

Pull Request - State: closed - Opened by Vince-janv about 2 months ago - 3 comments

#3565 - Generate samplesheets for raredisease with both lane number and flowcell

Issue - State: open - Opened by ramprasadn about 2 months ago - 1 comment

#3564 - fix PacBio sequencing run column names

Pull Request - State: closed - Opened by diitaz93 about 2 months ago - 2 comments
Labels: alembic migration

#3563 - Bug: No delivery option not parsed correctly.

Issue - State: open - Opened by islean about 2 months ago
Labels: Bug, Urgency M

#3562 - rename dir

Pull Request - State: closed - Opened by ChrOertlin about 2 months ago - 1 comment

#3561 - Rename order status

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

#3560 - Raredisease store d4 file

Pull Request - State: closed - Opened by rannick about 2 months ago - 1 comment

#3559 - update paths to match pipeline

Pull Request - State: closed - Opened by rannick about 2 months ago - 1 comment

#3558 - Rd add save mapped

Pull Request - State: closed - Opened by rannick about 2 months ago - 2 comments

#3557 - Handle EntryNotFoundError instead of ValueError when deleting Illumina flow cell

Pull Request - State: closed - Opened by karlnyr about 2 months ago - 1 comment

#3556 - Handle EntryNotFoundError when retrieving Illumina sequencing run by device internal ID

Pull Request - State: closed - Opened by karlnyr about 2 months ago - 2 comments

#3555 - Bug: Cannot post-process sequencing runs due to flawed logic

Issue - State: closed - Opened by karlnyr about 2 months ago
Labels: Bug, Gain L, Effort S, Urgency L

#3554 - Add type hints

Pull Request - State: closed - Opened by islean about 2 months ago - 1 comment

#3553 - add(microbialfastqsample orderin)

Pull Request - State: closed - Opened by ChrOertlin about 2 months ago - 1 comment

#3552 - Use list indices instead of case/sample names

Pull Request - State: closed - Opened by islean about 2 months ago - 1 comment

#3550 - Fix rna upload with dna case

Pull Request - State: closed - Opened by henrikstranneheim about 2 months ago - 4 comments

#3549 - Refactor flow cells endpoint

Pull Request - State: closed - Opened by seallard about 2 months ago - 1 comment

#3547 - Extract user endpoints

Pull Request - State: closed - Opened by seallard about 2 months ago - 1 comment

#3546 - Extract analyses endpoints

Pull Request - State: closed - Opened by seallard about 2 months ago - 1 comment

#3540 - Add clinical-delivery upload for raredisease

Pull Request - State: closed - Opened by rannick about 2 months ago - 2 comments
Labels: raredisease

#3539 - Add gens upload for raredisease

Pull Request - State: closed - Opened by rannick about 2 months ago - 2 comments
Labels: raredisease

#3536 - Bug: CLI command rna-to-scout not checking if case is an RNA case

Issue - State: closed - Opened by eliottBo about 2 months ago
Labels: Bug

#3535 - Add information on pool and corresponding samples to cg

Issue - State: open - Opened by beatrizsavinhas about 2 months ago - 2 comments
Labels: Gain M, cg, Urgency M

#3534 - Add genotype upload for raredisease

Pull Request - State: open - Opened by rannick about 2 months ago - 1 comment

#3533 - Add CLI to create validation cases

Issue - State: open - Opened by fevac about 2 months ago
Labels: Gain L, Urgency M, Needs Refinement

#3524 - Instantiate TicketHandler with freshdesk client

Pull Request - State: closed - Opened by ahdamin 2 months ago - 2 comments

#3512 - No tests for order endpoints

Issue - State: closed - Opened by seallard 2 months ago - 1 comment

#3473 - Extend Lims sample model

Pull Request - State: open - Opened by henrikstranneheim 2 months ago - 1 comment

#3471 - Bug: Raredisease workflow not storing Clinical STRs variants file

Issue - State: open - Opened by ivadym 2 months ago - 1 comment
Labels: Bug

#3470 - Bug: Raredisease not storing d4 coverage file

Issue - State: closed - Opened by ivadym 2 months ago - 1 comment
Labels: Bug

#3453 - feature(dev-branch-pacbio)

Pull Request - State: closed - Opened by ChrOertlin 3 months ago - 5 comments

#3444 - feat(rm): _add_missing_reads

Pull Request - State: closed - Opened by henrikstranneheim 3 months ago - 8 comments

#3439 - List finished analyses in the delivery message for data_delivery="analysis"

Issue - State: open - Opened by beatrizsavinhas 3 months ago
Labels: Enhancement, Gain S, Effort S, Urgency M

#3433 - Replace DeliverAPI with DeliveryAPI

Issue - State: closed - Opened by ivadym 3 months ago - 1 comment
Labels: Gain M, Effort M, Urgency M, Needs Refinement

#3431 - feat(rm): pkg_resource

Pull Request - State: open - Opened by henrikstranneheim 3 months ago - 7 comments

#3417 - Add price information to the sample table in cg

Issue - State: closed - Opened by pbiology 3 months ago - 5 comments
Labels: Enhancement, Needs Refinement, on hold

#3408 - Balsamic v16 release

Pull Request - State: open - Opened by ivadym 3 months ago - 1 comment

#3397 - Return case_ids per category

Pull Request - State: closed - Opened by islean 3 months ago - 3 comments

#3395 - Add a new field "Platform" to Application in statusdb

Issue - State: open - Opened by annagellerbring 3 months ago - 9 comments

#3393 - Remove pandas from gsaid api

Pull Request - State: open - Opened by henrikstranneheim 3 months ago - 7 comments

#3338 - Create orderflow for microbial sequencing only

Issue - State: open - Opened by Vince-janv 4 months ago - 4 comments

#3334 - Delivery error for fastq file not present in hk bundle does not include sample_id

Issue - State: closed - Opened by beatrizsavinhas 4 months ago

#3314 - Gens not available for some cases

Issue - State: closed - Opened by ElekCMMS 4 months ago - 5 comments

#3300 - Add mutant qc

Pull Request - State: closed - Opened by beatrizsavinhas 4 months ago - 8 comments

#3240 - Update filename for software versions

Pull Request - State: open - Opened by sofstam 5 months ago - 2 comments

#3212 - Add scout support for tomte

Pull Request - State: open - Opened by fevac 5 months ago - 8 comments

#3167 - Revise behaviour of get_aggregated_panels, document behaviour and refactor if needed

Issue - State: closed - Opened by fevac 6 months ago - 3 comments
Labels: Needs Refinement

#3163 - Update LIMS API

Issue - State: closed - Opened by ivadym 6 months ago - 1 comment
Labels: Gain M, Effort S, Urgency S

#3158 - inconsistency between percentage of duplicates in rnafusion

Issue - State: open - Opened by fevac 6 months ago - 3 comments
Labels: rnafusion

#3140 - Sequencing date for externally sequenced sample

Issue - State: closed - Opened by seallard 6 months ago - 1 comment

#3115 - Get delivery message for fluffy manual reruns retrieves wrong link to Statina

Issue - State: open - Opened by beatrizsavinhas 6 months ago - 2 comments
Labels: Good first issue, Gain S, Effort S, Urgency S

#3083 - Non-existent run parameters file raises an error

Issue - State: closed - Opened by diitaz93 6 months ago - 1 comment
Labels: demultiplex

#3076 - Create Taxprofiler order flow

Issue - State: open - Opened by Vince-janv 6 months ago - 1 comment

#3073 - Duplicate case sample filters base queries

Issue - State: closed - Opened by seallard 6 months ago - 1 comment

#3068 - (feat taxprofiler): Add taxprofiler-past-run-dirs command

Pull Request - State: closed - Opened by sofstam 6 months ago - 3 comments

#3064 - clean `scout-finished-cases` has a potential issue with old `solved` cases

Issue - State: closed - Opened by dnil 7 months ago - 11 comments
Labels: on hold

#3058 - Add uncancel action

Issue - State: open - Opened by beatrizsavinhas 7 months ago - 16 comments
Labels: Gain M, Effort S, cg, Urgency M, feature

#3035 - Order validation rules

Issue - State: closed - Opened by seallard 7 months ago - 4 comments
Labels: documentation

#3027 - Extract authentication service

Issue - State: closed - Opened by seallard 7 months ago - 1 comment

#3020 - Add validation of well positions

Issue - State: open - Opened by islean 7 months ago - 2 comments

#2999 - Review secrets management

Issue - State: closed - Opened by seallard 7 months ago - 1 comment
Labels: security

#2998 - Split the options endpoint

Issue - State: open - Opened by islean 7 months ago

#2997 - Review authentication between services

Issue - State: closed - Opened by seallard 7 months ago - 1 comment
Labels: security

#2996 - Stage creating tickets in production

Issue - State: closed - Opened by seallard 7 months ago - 1 comment
Labels: developer-experience

#2916 - Rna upload service starting every 10th minute?

Issue - State: closed - Opened by seallard 8 months ago - 1 comment
Labels: mip-rna

#2906 - Filter for "Capture kit"

Issue - State: open - Opened by annagellerbring 8 months ago
Labels: Good first issue

#2871 - Ensure data for negative controls is delivered to customers

Issue - State: closed - Opened by karlnyr 8 months ago - 10 comments
Labels: Gain L, Effort S, Urgency M

#2852 - Remove analysis model in status db

Issue - State: closed - Opened by seallard 9 months ago - 1 comment
Labels: Needs Refinement, Refactor

#2851 - Update to sars-cov2 ordering and upload

Issue - State: closed - Opened by Vince-janv 9 months ago - 2 comments

#2842 - Organise demultiplex tests and fixtures around only 7 flow cell cases

Issue - State: closed - Opened by diitaz93 9 months ago - 3 comments
Labels: Refactor, demultiplex, Test coverage

#2819 - Move tests from root conftest to fixture plugins directory

Issue - State: closed - Opened by diitaz93 9 months ago - 1 comment
Labels: help wanted

#2801 - Not compressible samples are being compressed

Issue - State: open - Opened by ivadym 9 months ago - 10 comments
Labels: Bug, Gain L, Effort M, Urgency L, bioinfo-dev

#2796 - Refactor delivery api

Pull Request - State: open - Opened by seallard 9 months ago - 1 comment

#2795 - Slow upload command

Issue - State: open - Opened by seallard 9 months ago

#2794 - Parallelize tests

Pull Request - State: closed - Opened by seallard 9 months ago - 1 comment

#2793 - feat(Nanopore) Database model for Nanopore runs

Pull Request - State: open - Opened by Vince-janv 9 months ago - 2 comments

#2792 - Update database to fit new sequencing technologies

Issue - State: open - Opened by Vince-janv 9 months ago
Labels: Project Task

#2791 - feat(Nanopore) Check manifest file to confirm data transfer

Pull Request - State: open - Opened by Vince-janv 9 months ago - 1 comment
Labels: Project Task

#2790 - feat(is_deleted): remove

Pull Request - State: open - Opened by henrikstranneheim 9 months ago - 1 comment
Labels: Enhancement

#2789 - feat(Nanopore) Re-write create manifest command to support Nanopore structure

Pull Request - State: closed - Opened by Vince-janv 9 months ago - 2 comments

#2788 - feat(sql): Refactor addhandler

Pull Request - State: open - Opened by henrikstranneheim 9 months ago - 1 comment
Labels: Enhancement

#2787 - Check transfer of Nanopore data to server

Issue - State: open - Opened by Vince-janv 9 months ago
Labels: Project Task

#2786 - Remove is uploaded to vogue

Pull Request - State: open - Opened by henrikstranneheim 9 months ago - 1 comment
Labels: Enhancement

#2785 - Export new concentration field

Pull Request - State: open - Opened by islean 10 months ago - 2 comments

GitHub / Clinical-Genomics/cg issues and pull requests