Clinical-Genomics/cg issues and pull requests

#2016 - Add structure for parsing of sequencing metrics

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

#2015 - Completely replace genotype with genotype-api

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

#2014 - Only call methods in stats api

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

#2013 - Remove get_unaligned_id

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

#2012 - Move models and find methods in cg stats

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

#2011 - Add where to archive data in StatusDB

Issue - State: closed - Opened by henrikstranneheim over 1 year ago - 9 comments
Labels: Needs Refinement

#2010 - Add sequenced data type per customer to StatusDB

Issue - State: open - Opened by henrikstranneheim over 1 year ago - 2 comments
Labels: Needs Refinement

#2009 - Add validation cases from balsamic to skip compression

Pull Request - State: closed - Opened by mathiasbio over 1 year ago - 3 comments

#2008 - Database connection dropped

Issue - State: closed - Opened by seallard over 1 year ago - 4 comments

#2007 - 2000 - Use cg.utils.enums instead of cgmodels

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

#2006 - fix(RNA-upload - remove update argument)

Pull Request - State: closed - Opened by karlnyr over 1 year ago - 6 comments

#2005 - adding mobile element files to scout load

Pull Request - State: closed - Opened by jemten over 1 year ago - 3 comments

#2004 - Remove unused CLI functions and subfunctions only used in them

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

#2003 - Modify existing flow cell and Sample Sheet Creator for NovaSeqXPlus

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

#2002 - patch(CLI) descriptive function names in CLI

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

#2001 - Replace redundant methods in stats

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

#2000 - Migrate StrEnum class from cgmodels to cg

Issue - State: closed - Opened by diitaz93 over 1 year ago - 3 comments
Labels: Good first issue

#1999 - Rm pdc spring archive

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

#1998 - feat(taxprofiler): Add config case

Pull Request - State: open - Opened by sofstam over 1 year ago - 2 comments
Labels: cg, Project Task, taxprofiler

#1997 - feat(rnafusion): add qc checks

Pull Request - State: closed - Opened by fevac over 1 year ago - 5 comments
Labels: rnafusion

#1996 - add(sequencing_stats model)

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

#1995 - Modify run parameter model and tests

Pull Request - State: closed - Opened by diitaz93 over 1 year ago - 3 comments

#1994 - change(rnafusion): refactor multiqc related methods to MultiQC class

Issue - State: open - Opened by fevac over 1 year ago
Labels: cg, rnafusion

#1993 - fix(rnafusion): start with dry_run

Pull Request - State: closed - Opened by rannick over 1 year ago - 1 comment
Labels: rnafusion

#1992 - Remove unused method sample from stats API

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

#1991 - Rename functions used for CLI commands to more descriptive names

Issue - State: closed - Opened by Vince-janv over 1 year ago
Labels: Good first issue

#1990 - Add new LIMS API functions to fetch RNA data

Pull Request - State: closed - Opened by Karl-Svard over 1 year ago - 1 comment

#1989 - Refactor method for creating a novaseq flow cell

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

#1988 - refactoring RNA collaborator filtering function

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

#1987 - exclude cg-dragen2

Pull Request - State: closed - Opened by karlnyr over 1 year ago - 2 comments

#1986 - Remove unused requirements and add transitive ones

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

#1985 - Move exist methods from stats models

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

#1984 - feat(rnafusion) add metrics deliverables

Pull Request - State: closed - Opened by fevac over 1 year ago - 3 comments
Labels: rnafusion

#1983 - Incorporate sample sheet validation code from cgmodels in cg

Pull Request - State: closed - Opened by diitaz93 over 1 year ago - 3 comments

#1982 - fix(rnafusion): arriba report upload to scout

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

#1981 - Fix(Scout upload): normal samples as tumors

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

#1980 - feat(rnafusion): add starfusion cram to deliverables

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

#1979 - Add cram to rnafusion deliverables

Issue - State: closed - Opened by fevac over 1 year ago
Labels: rnafusion

#1978 - #1870: Add test verifying that RNA case upload fails when the associated DNA case has not been sequenced

Pull Request - State: open - Opened by seallard over 1 year ago - 1 comment

#1977 - Automatic re-upload of existing rna-analysis to "primary analyses"

Issue - State: open - Opened by karlnyr over 1 year ago
Labels: Gain M, Effort M, Urgency S, Needs Refinement

#1976 - Update sample sheet for NovaSeqX

Pull Request - State: closed - Opened by diitaz93 over 1 year ago - 1 comment

#1975 - feat(Archiving) Adds archive integration for samples

Pull Request - State: open - Opened by Vince-janv over 1 year ago - 1 comment

#1974 - fix(rnafusion): change default value for FUSIONREPORT_FILTER

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

#1973 - Fix database session management

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

#1972 - Normal samples analysed as tumor in balsamic have no variants after upload to Scout

Issue - State: closed - Opened by mathiasbio over 1 year ago - 2 comments
Labels: Scout, Balsamic, Gain M, Effort S, Urgency M

#1971 - RNAfusion: add validation cases to avoid compression

Issue - State: closed - Opened by fevac over 1 year ago
Labels: rnafusion

#1970 - RNAfusion: config-case abort if no fastq files are found

Issue - State: open - Opened by fevac over 1 year ago
Labels: Effort S, rnafusion

#1969 - Move find functions into FindHandler class

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

#1968 - Introduce Skip-rc option

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

#1967 - change(rnafusion): change default parameters

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

#1966 - Add missing to_dict methods

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

#1965 - Add elements for v2 sample sheet

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

#1964 - Revert "feat(skip-rc-qc) Add option to skip qc to orders"

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

#1963 - Remove alchy from stats wip

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

#1962 - Fix broken database interaction

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

#1961 - RNAfusion: add clinical delivery upload

Issue - State: closed - Opened by fevac over 1 year ago - 3 comments
Labels: rnafusion

#1960 - feat(rnafusion): Add default compute environment and revision

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

#1959 - RNAfusion: cleanup options and refine structure

Issue - State: open - Opened by fevac over 1 year ago - 1 comment
Labels: rnafusion, on hold

#1958 - Remove models from base handler

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

#1957 - RNAfusion: Add command for references download

Issue - State: closed - Opened by fevac over 1 year ago - 1 comment
Labels: cg, rnafusion

#1956 - Replace alchy with sqlalchemy in housekeeper

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

#1954 - Refactor validate sample sheet

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

#1953 - Fix stats model imports

Pull Request - State: closed - Opened by seallard over 1 year ago - 1 comment
Labels: Project Task

#1951 - Remove unused functions in cg stats

Pull Request - State: closed - Opened by seallard over 1 year ago - 2 comments
Labels: Project Task

#1932 - Rename cli set command family to case

Pull Request - State: closed - Opened by diitaz93 over 1 year ago - 4 comments
Labels: Project Task

#1925 - Add validation cases to skip compression

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

#1918 - update(HK API functions)

Pull Request - State: closed - Opened by ChrOertlin over 1 year ago - 2 comments
Labels: Project Task

#1906 - RNAfusion: set default params

Issue - State: closed - Opened by fevac over 1 year ago
Labels: Effort S, rnafusion

#1905 - RNAfusion: specify --compute-env

Issue - State: closed - Opened by fevac over 1 year ago
Labels: Effort S, rnafusion

#1901 - Add testmon to action

Pull Request - State: closed - Opened by henrikstranneheim over 1 year ago - 7 comments

#1887 - Speed up pytests

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

#1886 - Duplicate endpoints

Issue - State: open - Opened by seallard over 1 year ago - 3 comments

#1880 - Upload research variants to Scout for Balsamic UMI

Issue - State: closed - Opened by ivadym over 1 year ago - 3 comments
Labels: Balsamic, Needs Refinement

#1870 - Bug in upload of RNA cases to Scout

Issue - State: open - Opened by SofiaOtero over 1 year ago - 6 comments

#1869 - Inconsistent database models

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

#1866 - RNAfusion: lock version when using tower

Issue - State: closed - Opened by fevac over 1 year ago
Labels: Gain M, Effort S, rnafusion

#1862 - Ambiguous use of name property on Family model

Issue - State: closed - Opened by seallard over 1 year ago - 1 comment
Labels: Bug

#1855 - Add Balsamic validation cases

Issue - State: closed - Opened by fevac over 1 year ago - 2 comments
Labels: Balsamic

#1842 - Generate delivery reports for downsampled samples

Issue - State: open - Opened by beatrizsavinhas over 1 year ago - 6 comments

#1827 - feat(taxprofiler): Add taxprofiler as an option to cg workflow

Pull Request - State: closed - Opened by sofstam over 1 year ago - 5 comments
Labels: cg, Project Task, taxprofiler

#1822 - Refer to database id:s in a consistent manner throughout the codebase

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

#1817 - _add_missing_reads function not working

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

#1812 - feat(skip-rc-qc) Add option to skip qc to orders

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

#1807 - Handle orders from order portal with "Bypass reception control"

Issue - State: closed - Opened by pbiology over 1 year ago - 2 comments
Labels: Needs Refinement

#1802 - Refactor structure of handlers

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

#1794 - Refactor long methods and parameter lists

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

#1782 - Upload MIP-RNA to all DNA cases in collaborator group matching by subject_ID

Pull Request - State: closed - Opened by peterpru over 1 year ago - 3 comments
Labels: MIP, cg, Project Task

#1762 - RNAfusion: fix arriba upload in Scout

Issue - State: closed - Opened by fevac over 1 year ago
Labels: Bug, rnafusion, Project Task

#1732 - Slow CLI commands

Issue - State: open - Opened by seallard over 1 year ago - 10 comments
Labels: Enhancement

#1720 - RNAfusion: Add delivery report

Issue - State: open - Opened by fevac over 1 year ago - 13 comments
Labels: Needs Refinement, rnafusion, Project Task

#1715 - Flowcell H7537DSXY stuck on retrieved, even though it finished demultiplexing

Issue - State: closed - Opened by gustavlagneborg over 1 year ago - 5 comments
Labels: Bug

#1709 - Family, sample, and capture kit relationship (samples with different capture kits in a family)

Issue - State: closed - Opened by ivadym over 1 year ago - 1 comment
Labels: cg, Needs Refinement

#1648 - Add a "validate" step before storage to microSALT and Mutant

Issue - State: closed - Opened by Vince-janv almost 2 years ago - 3 comments
Labels: Gain L, Effort L, production, Project Task

#1640 - feat(external data) Re-writing of the external-data module

Pull Request - State: closed - Opened by Vince-janv almost 2 years ago - 3 comments

#1635 - fix(microSALT delivery) Change delivery types and tags for microSALT

Pull Request - State: closed - Opened by Vince-janv almost 2 years ago - 3 comments

#1631 - Requests for update of 1508 ordeform

Issue - State: closed - Opened by Vince-janv almost 2 years ago - 4 comments
Labels: Gain S, Urgency S, Customer request, customer-experience, on hold

#1618 - RNA(Add upload of multiqc to Scout)

Pull Request - State: closed - Opened by karlnyr almost 2 years ago - 10 comments
Labels: Gain M, Effort S, Urgency M

#1602 - Deliver nextclade output as part of MUTANT deliverables

Issue - State: closed - Opened by pbiology almost 2 years ago - 3 comments
Labels: Project Task

#1600 - Subject_ID not enough to distinguish samples

Issue - State: closed - Opened by peterpru almost 2 years ago - 3 comments
Labels: Gain S, Effort M, Urgency M, mip-rna

#1563 - Delivery report for Balsamic QC only analysis

Issue - State: closed - Opened by ivadym about 2 years ago
Labels: Balsamic, Gain M, Effort S, Urgency L, feature

GitHub / Clinical-Genomics/cg issues and pull requests