Clinical-Genomics/cg issues and pull requests

#3688 - fix(clinical delivery call)

Pull Request - State: open - Opened by ChrOertlin about 1 month ago - 1 comment

#3687 - add raredisease pedigree check

Pull Request - State: open - Opened by peterpru about 1 month ago - 1 comment

#3686 - Fix names of alembic scripts

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

#3685 - Remove unused Sample properties

Pull Request - State: closed - Opened by beatrizsavinhas about 1 month ago - 1 comment

#3684 - feat(test for counting reads of negative controls)

Pull Request - State: closed - Opened by beatrizsavinhas about 1 month ago - 1 comment

#3683 - (Improve order flow) Add Balsamic validation rules

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

#3682 - feat(count all reads of negative controls)

Pull Request - State: closed - Opened by beatrizsavinhas about 1 month ago - 1 comment

#3681 - feat(store all fastq files for negative controls)

Pull Request - State: closed - Opened by beatrizsavinhas about 1 month ago - 1 comment

#3680 - Add q30 check when calculating sample reads

Pull Request - State: closed - Opened by beatrizsavinhas about 1 month ago - 1 comment

#3679 - Calculation for sample reads does not account for low q30 score

Issue - State: closed - Opened by beatrizsavinhas about 1 month ago - 1 comment
Labels: Bug, Effort S, Urgency L

#3677 - Hide development analyses

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

#3676 - rename fastq workflow to 'raw-data'

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

#3671 - (Improve order flow) Fix workflow models

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

#3670 - Make cg help searchable

Issue - State: open - Opened by seallard about 1 month ago

#3668 - Feat(ticketing) Use Freshdesk

Pull Request - State: open - Opened by ahdamin about 1 month ago - 1 comment

#3667 - (Improve order flow) Make sure internal_id None is disregarded

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

#3666 - (Improve order flow) Populate needed values

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

#3665 - Add balsamic sample sex validation

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

#3664 - Remove unnecessary rules

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

#3663 - Add balsamic validation rules

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

#3662 - Add balsamic

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

#3661 - Patch sequencing_started_at

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

#3660 - Bug: Fetching sequencing runs break

Issue - State: closed - Opened by islean about 1 month ago
Labels: Bug

#3659 - Create service to upload completed mutant analyses to caesar

Issue - State: open - Opened by beatrizsavinhas about 1 month ago
Labels: Gain M, Effort S, Urgency S

#3658 - Create service mutant-store-available

Issue - State: closed - Opened by beatrizsavinhas about 1 month ago - 1 comment
Labels: Good first issue, Gain M, Effort S, Urgency M

#3657 - Add mutant order validation rules

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

#3656 - Add mutant rules

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

#3655 - Update contact person for invoicing workflow

Issue - State: open - Opened by annagellerbring about 1 month ago - 1 comment
Labels: Urgency L

#3654 - (Improve order flow) Add MutantSample model

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

#3653 - Add mutant order validation skeleton

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

#3652 - (Improve order flow) Remove existing sample rule for microsalt

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

#3651 - Delivery on sample level of fastq files to Caesar

Issue - State: open - Opened by karlnyr about 1 month ago
Labels: Gain M, Effort M, Urgency S

#3650 - Delivery report - add standard sentence for when QC metrics has failed.

Issue - State: open - Opened by AnnaLeinfelt about 1 month ago

#3649 - (Improve order flow)Add existing sample/case models and separate flows

Issue - State: closed - Opened by islean about 1 month ago - 1 comment

#3648 - Add models for existing samples and cases

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

#3647 - add(delivery service factory)

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

#3646 - Rename managed_variants file to critical variants?

Issue - State: open - Opened by jemten about 1 month ago - 1 comment

#3645 - Create trailblazer analysis with workflow id

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

#3644 - Perform validation before ticket creation

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

#3643 - Bug: Application Versions with malformed `updated_at`

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

#3642 - Bug: Tickets are submitted despite incorrect case names

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

#3641 - Feat(rsync) Remove -t flag for sars-cov

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

#3640 - Fix(rsync) Remove sars-cov -t flag

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

#3639 - (Improve order flow) Type panels as string

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

#3638 - Feat(ticketing) Remove Osticket

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

#3637 - Patch samples-in-collaboration endpoint

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

#3636 - Bug: Tumour samples are not read as such in the order portal

Issue - State: closed - Opened by islean about 1 month ago
Labels: Bug

#3635 - (Improve order flow) Remove subject id from tomte

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

#3634 - Feat/rm os ticket

Pull Request - State: closed - Opened by ahdamin about 1 month ago - 1 comment

#3633 - Patch tissue block typing

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

#3632 - Add empty string to None conversion

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

#3631 - Improve delivery report pytests

Pull Request - State: open - Opened by ivadym about 1 month ago - 5 comments

#3630 - (Improve order flow) Patch min string length

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

#3629 - Make sure ordered_at is evaluated at persist

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

#3628 - Bug: Ordered_at dates are not updated

Issue - State: closed - Opened by islean about 1 month ago
Labels: Bug

#3627 - Re-write delivery api

Issue - State: open - Opened by ChrOertlin about 1 month ago

#3626 - add(delivery file formatter)

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

#3625 - Add mip dna rules

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

#3624 - (Improve order flow) Refactor util methods

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

#3623 - wip

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

#3622 - feat(delivery file mover service)

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

#3621 - Remove tomte from general rules

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

#3620 - feat/connect order to Freshdesk ticket

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

#3619 - Add dev endpoints

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

#3618 - Improve order flow main

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

#3617 - (Improve order flow) Ensure buffer is set for new samples

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

#3616 - (Improve order flow) Add extraction method validation

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

#3615 - Add mip dna skeleton

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

#3614 - Add backend validation for mip-dna orders

Issue - State: closed - Opened by seallard about 2 months ago

#3613 - Add organism exists validation for microSALT

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

#3612 - (Improve order flow) Validate volume interval for microSALT

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

#3611 - (Improve order flow) Add validation of repeated sample names for Microsalt

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

#3610 - (Improve order flow) Validate samples exist microsalt

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

#3609 - Improve order flow main

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

#3608 - (Improve order flow) Fix placement of Tomte rule

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

#3607 - Bug: Housekeeper

Issue - State: closed - Opened by RasmusBurge-CG about 2 months ago - 1 comment
Labels: Bug

#3606 - fix(RNAfusion scout conversion)

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

#3605 - Validate plate samples have a well assigned

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

#3604 - Add microsalt max one sample per well validation

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

#3603 - (Improve order flow) Add microsalt validate application not archived

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

#3602 - Validate microsalt app compatibility

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

#3601 - add(fetch delivery files service)

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

#3600 - (Improve order flow) Add sample application exists validation

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

#3599 - Shuffle error models

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

#3598 - feat(new delivery flow)

Pull Request - State: open - Opened by ChrOertlin about 2 months ago - 6 comments

#3597 - (Improve order flow) Add order validation rules for microsalt

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

#3596 - Add missing user endpoints

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

#3595 - Add microsalt order validation skeleton

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

#3594 - (Improve order flow) Add order validation response test

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

#3593 - Add backend validation for microsalt orders

Issue - State: closed - Opened by seallard about 2 months ago

#3592 - Further improve order submitters

Issue - State: open - Opened by ChrOertlin about 2 months ago
Labels: Gain L, Effort M, Urgency S

#3591 - Add raredisease scout upload

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

#3590 - Cancel actions creates orders without cases

Issue - State: open - Opened by seallard about 2 months ago - 2 comments
Labels: Bug

#3589 - Map order errors to response

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

#3588 - (Improve order flow) Make source optional

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

#3587 - (Improve order flow) Remove delivery type from Case

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

#3586 - (Improve order flow) Patch validate fathers are male

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

#3585 - Fix pedigree validation

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

#3584 - Fix mother sex validation

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

#3583 - Validate existing fathers

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

GitHub / Clinical-Genomics/cg issues and pull requests