Ecosyste.ms: Issues

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GitHub / Clinical-Genomics/cg issues and pull requests

#2784 - underscores in sample internal_ids issues for balsamic

Issue - State: open - Opened by mathiasbio 11 months ago
Labels: Urgency M, Needs Refinement

#2783 - Bump paramiko from 3.3.1 to 3.4.0

Pull Request - State: open - Opened by dependabot[bot] 11 months ago - 1 comment
Labels: dependencies

#2782 - Refactor sample sequencing QC logic

Pull Request - State: open - Opened by karlnyr 11 months ago - 1 comment

#2781 - Update rules for V2 sample sheet generation for HiSeq flow cell compatibility

Issue - State: closed - Opened by diitaz93 11 months ago
Labels: demultiplex

#2780 - Refactor gender to sex

Pull Request - State: closed - Opened by henrikstranneheim 11 months ago - 3 comments
Labels: Enhancement

#2779 - Change tuple to set for panel combo

Pull Request - State: closed - Opened by seallard 11 months ago - 1 comment

#2778 - mip-dna case cannot be started due to panel issue

Issue - State: closed - Opened by seallard 11 months ago
Labels: Bug, Gain M, Effort S, Urgency L

#2777 - feat(refactor): family

Pull Request - State: closed - Opened by henrikstranneheim 11 months ago - 1 comment
Labels: Enhancement

#2776 - Add columns

Pull Request - State: closed - Opened by islean 11 months ago - 5 comments

#2775 - feat(clean): Do not abort but continue

Pull Request - State: closed - Opened by henrikstranneheim 11 months ago - 3 comments
Labels: Bug

#2774 - Treat panel abbrevs as case sensitive

Issue - State: closed - Opened by seallard 12 months ago - 1 comment

#2773 - Add workflow protected tags for rnafusion

Pull Request - State: closed - Opened by fevac 12 months ago - 2 comments

#2772 - Clean up run_analysis method for nf_analysis

Pull Request - State: closed - Opened by fevac 12 months ago - 4 comments

#2771 - Redefine flow cell and sequencing data status

Issue - State: open - Opened by henrikstranneheim 12 months ago
Labels: Gain L, Effort L, Urgency M, Needs Refinement

#2770 - Pre analysis check

Issue - State: open - Opened by karlnyr 12 months ago
Labels: Enhancement, Gain M, Effort S, Urgency M

#2769 - Fix bug causing mip workflow start to fail

Pull Request - State: closed - Opened by seallard 12 months ago - 2 comments

#2768 - MIP workflow start fails for specific case

Issue - State: closed - Opened by seallard 12 months ago
Labels: Bug, Gain M, Effort S, Urgency L

#2767 - Update tower binary

Pull Request - State: closed - Opened by fevac 12 months ago - 3 comments

#2766 - (Archiving) Refactor DDN flow

Pull Request - State: closed - Opened by islean 12 months ago - 3 comments

#2765 - Set priority for tower compute environment

Pull Request - State: closed - Opened by fevac 12 months ago - 6 comments

#2764 - Handle cfDNA concentration

Issue - State: closed - Opened by islean 12 months ago - 1 comment

#2763 - Refactor link fastq files

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 3 comments
Labels: Enhancement, Project Task

#2762 - Remove cg / hermes redundancy

Issue - State: open - Opened by fevac 12 months ago - 1 comment
Labels: Needs Refinement

#2761 - Add panel Inherited cancer to the clinical masterlist

Pull Request - State: closed - Opened by beatrizsavinhas 12 months ago - 3 comments

#2760 - (Archiving) delete files

Pull Request - State: closed - Opened by islean 12 months ago - 5 comments

#2759 - rnafusion HK tags as constants

Pull Request - State: closed - Opened by fevac 12 months ago - 5 comments

#2758 - Add column to determine if eligible for skip qc

Pull Request - State: closed - Opened by islean 12 months ago - 5 comments

#2757 - Added method get_managed_variants to mip rna workflow

Pull Request - State: closed - Opened by diitaz93 12 months ago - 2 comments

#2756 - Clean directories of old cancelled cases

Issue - State: open - Opened by fevac 12 months ago - 1 comment

#2755 - feat(refactor): Remove deprecated code

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 2 comments

#2754 - Add automatic quality control of analyses for microbial samples

Pull Request - State: closed - Opened by seallard 12 months ago - 5 comments

#2753 - Add all files uploaded to scout in delivery report

Issue - State: open - Opened by fevac 12 months ago

#2752 - Patch broken enums

Pull Request - State: closed - Opened by islean 12 months ago - 5 comments

#2751 - Update flow cell readiness check logging

Pull Request - State: closed - Opened by karlnyr 12 months ago - 2 comments

#2750 - Add export managed variants

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 4 comments
Labels: Project Task

#2748 - Update drop-down presets for flow cell status in statusdb

Issue - State: closed - Opened by Karl-Svard 12 months ago - 2 comments

#2746 - feat(ruff): Update

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 2 comments

#2745 - refactor nf_analysis get_deliverables to consider multiple samples

Issue - State: open - Opened by fevac 12 months ago - 1 comment

#2744 - mapped_reads as property

Issue - State: closed - Opened by fevac 12 months ago - 3 comments

#2743 - add class AnalysisSampleTags

Issue - State: closed - Opened by fevac 12 months ago

#2742 - Allow customers to use the same panel name

Issue - State: closed - Opened by seallard 12 months ago - 1 comment
Labels: customer-experience, Needs Refinement

#2740 - Parse new concentration field

Pull Request - State: closed - Opened by islean 12 months ago - 2 comments

#2739 - feat(black): Update

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 2 comments

#2738 - Remove deprecated field from the sample model

Issue - State: closed - Opened by seallard 12 months ago - 1 comment
Labels: Gain S, Effort M, Urgency S, backend

#2737 - (Archiving) Fix behaviour for non-positive limits

Pull Request - State: closed - Opened by islean 12 months ago - 4 comments

#2736 - Set BCLConvert as default in automation

Pull Request - State: closed - Opened by diitaz93 12 months ago - 10 comments
Labels: demultiplex

#2735 - (Archiving) Delete archived files via API

Issue - State: open - Opened by islean 12 months ago - 1 comment

#2734 - Feat(Orders) Merged metagenome orderform with others

Pull Request - State: closed - Opened by Vince-janv 12 months ago - 2 comments

#2733 - Fix verification of HTTPS requests

Pull Request - State: closed - Opened by islean 12 months ago - 3 comments

#2732 - Add raredisease run case

Pull Request - State: open - Opened by rannick 12 months ago - 1 comment
Labels: raredisease

#2731 - Deprecate constant BCLConvert.DRAGEN

Pull Request - State: closed - Opened by diitaz93 12 months ago - 2 comments
Labels: demultiplex

#2730 - (Archiving) Use tag when fetching spring files

Pull Request - State: closed - Opened by islean 12 months ago - 4 comments

#2728 - Write start-available tests for all pipelines

Issue - State: open - Opened by Vince-janv 12 months ago
Labels: help wanted

#2727 - Enable delivery of external samples

Pull Request - State: closed - Opened by seallard 12 months ago - 3 comments

#2726 - Add new development priority to cases

Pull Request - State: open - Opened by seallard 12 months ago - 1 comment

#2725 - add raredisease config

Pull Request - State: open - Opened by peterpru 12 months ago - 1 comment
Labels: raredisease

#2724 - Fix Sonarcloud issues

Pull Request - State: closed - Opened by seallard 12 months ago - 2 comments

#2723 - Remove balsamic r flag

Pull Request - State: closed - Opened by seallard 12 months ago - 4 comments

#2722 - Remove required -r option from cg workflow balsamic

Issue - State: closed - Opened by fevac 12 months ago - 2 comments

#2721 - Create application versions via admin ui

Pull Request - State: closed - Opened by seallard 12 months ago - 1 comment

#2720 - fix - catch sample sheet errors in sample sheet generation automation

Pull Request - State: closed - Opened by diitaz93 12 months ago - 3 comments
Labels: Bug, demultiplex

#2719 - add new priority "development" to cases

Issue - State: open - Opened by ChrOertlin 12 months ago - 1 comment
Labels: Needs Refinement

#2718 - Add raredisease panel cmd

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 8 comments
Labels: Project Task, raredisease

#2717 - (Archiving) Add archive location tag to spring files

Pull Request - State: closed - Opened by islean 12 months ago - 2 comments

#2716 - (Archiving) How to determine archive location for files

Issue - State: closed - Opened by islean 12 months ago - 7 comments

#2715 - feat(gpg): Answer yes for symmetric cmd

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 3 comments

#2714 - Bump cryptography from 41.0.4 to 41.0.6

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 3 comments
Labels: dependencies

#2713 - skip model validation for existing path

Pull Request - State: closed - Opened by fevac 12 months ago - 2 comments

#2712 - Refactor to pep0663

Pull Request - State: closed - Opened by henrikstranneheim 12 months ago - 4 comments
Labels: Enhancement

#2711 - Integration of taxprofiler and post-processing pipeline in cg

Issue - State: open - Opened by LilyAnderssonLee 12 months ago
Labels: Needs Refinement

#2710 - Fix fastq tag assignment from spring file

Pull Request - State: closed - Opened by diitaz93 12 months ago - 3 comments

#2709 - Spring file tags not being passed correctly to fastq files upon decompression

Issue - State: closed - Opened by diitaz93 almost 1 year ago
Labels: Bug

#2708 - fix(pytests) Clarify some tests and fixtures

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

#2707 - feat(encrypt): Answer yes in gpg encrypt and decrypt cmds

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

#2706 - Refactor to pep 0604

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

#2705 - Skip lims data retrieval if downsampled for rnafusion report

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

#2704 - Make delivery report mandatory for Scout uploads

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

#2703 - Add cg nas and encryption dir

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

#2702 - Deliveries and storage of incomplete analyses AND proper tracking of deliveries.

Issue - State: open - Opened by karlnyr about 1 year ago - 2 comments
Labels: Gain L, Urgency S

#2701 - (feat taxprofiler) Add metrics-deliver

Pull Request - State: open - Opened by sofstam about 1 year ago - 1 comment
Labels: cg, taxprofiler

#2700 - Run panel PANELAPP-GREEN by default in all MIP runs

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

#2699 - New orderform version

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

#2698 - Add PANELAPP-GREEN to all MIP runs, like OMIM-AUTO

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

#2697 - Export managed variants from scout

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

#2696 - At what step in the logic should we run QC checks?

Issue - State: open - Opened by karlnyr about 1 year ago - 2 comments
Labels: question, Gain M, Effort S, Needs Refinement

#2695 - Add panel combo as requested by cust002

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

#2694 - feat(encrypt_dir): Add and change current

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

#2693 - fix(has_backup): Timing

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

#2692 - (Archiving) Modify according to documentation

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

#2691 - Update current encryption dir path

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

#2690 - Count dsmc processes

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

#2689 - Add delivery report to Balsamic-QC workflow

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

#2688 - Add Balsamic validated metrics to delivery report

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

#2687 - Update gene_panel.py

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

#2685 - Cannot enter app tag into the version field on application in status-db

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