Clinical-Genomics / cg

Glue between Clinical Genomics apps

Clinical-Genomics/cg Issues

Pages in the `Sample Lane Sequencing Metrics` table are not disjoint
Closed a day ago2
No error warning when upload to gens fails
Updated a day ago10
Create orderflow for microbial sequencing only
Updated 4 days ago3
Revise behaviour of get_aggregated_panels, document behaviour and refactor if needed
Updated 7 days ago1
“non-hiseq-clinical”-users cannot use the decompress commmand.
Updated 7 days ago5
Harmonise microSALT delivery options
Updated 8 days ago
Calculation of case sequencing QC slows down /orders
Updated 8 days ago9
CreateHandler add_<record> functions only return model
Updated 8 days ago1
Add flexibility to the sample sheet validation
Updated 8 days ago4
Counting cases where `start` failed
Updated 8 days ago4
Support delivery message for "analysis" type
Updated 8 days ago8
Concise re-analysis of old cases
Updated 8 days ago1
Copy db + files to stage
Updated 8 days ago1
Upload mip analyses with different analysis types
Closed 8 days ago2
Alter the ordering of microbial samples
Updated 9 days ago7
A short, descriptive title.
Closed 9 days ago
Add optional parameters for cg downsample samples
Updated 10 days ago4
The is_latest_analysis_completed check is ignored for storage
Closed 11 days ago
Not exiting multi-case upload process when one gens upload fails
Updated 14 days ago3
Automatic decompression of samples when uploading
Updated 16 days ago2
Gens not available for some cases
Updated 17 days ago2
NEXTFLOW_WORKFLOWS constant(s) while developping pipelines
Closed 23 days ago6
Replace parameter yes with skip_confirmation
Updated 23 days ago
Empty folder creation when cloning cg repo
Closed 23 days ago1
Missing reference
Closed 24 days ago
multiqc_report not delivered for mip-dna cases
Closed 24 days ago2
No TB analysis is created for cases with no associated order even though jobs start running
Closed 25 days ago4
Add separate layer of serialization logic
Updated 25 days ago
Set reference genome for selected RNA samples
Closed a month ago4
Clash of '-d' flag in cli commands
Closed a month ago6
Add relationships to parent classes
Closed a month ago
Speedup test action
Closed a month ago7
Add tissue check before uploading to loqus
Closed a month ago8
Analysis API tied to workflow on instantiation
Closed a month ago5
Restricting special characters for case name
Closed a month ago
Update delivery report for taxprofiler
Closed a month ago
Incorrect analysis started_at fields in Statusdb
Updated a month ago5
Reference genome not saved in database
Updated a month ago
Fix delivery report to get metrics from all lanes
Closed a month ago1
Make raredisease orderable
Updated a month ago1
Allow fetching archived files via CLI
Closed 2 months ago1
Delivery report for taxprofiler
Closed 2 months ago
sars-cov-2 still available as option in order table
Closed 2 months ago
Find better names for archive locations
Updated 2 months ago
Is code for demultiplexing on sequencer still relevant?
Closed 2 months ago3
Update LIMS API
Updated 2 months ago
inconsistency between percentage of duplicates in rnafusion
Updated 2 months ago
Limit number of cases fetched to be started.
Closed 2 months ago5
Sequencing date for externally sequenced sample
Updated 2 months ago
Mark old orders as delivered
Closed 2 months ago4