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40 Open 83 Closed
40 Open 83 Closed
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Issues list

Invalid Cohort IDs as inputs fails silently core Changes to the cpg-workflows api
#768 opened May 24, 2024 by vivbak
@vivbak
STRipy stage fixes and improvements bug Something isn't working enhancement New feature or request rare disease Change is exclusively within the scope of the rare disease pipeline
#757 opened May 21, 2024 by EddieLF
4 tasks
2
gCNV JointSegmentation Issues rare disease Change is exclusively within the scope of the rare disease pipeline
#740 opened May 10, 2024 by MattWellie
@MattWellie
1
Improve robustness of Seqr Loader MergeVCFs job rare disease Change is exclusively within the scope of the rare disease pipeline
#739 opened May 9, 2024 by EddieLF
3 tasks
1
Exome calling lists include chrM rare disease Change is exclusively within the scope of the rare disease pipeline
#735 opened May 8, 2024 by MattWellie
@cassimons @EddieLF @vivbak
3
New stage for long-read sequencing data: BamToCram rare disease Change is exclusively within the scope of the rare disease pipeline
#732 opened May 7, 2024 by EddieLF
1
Exomiser - Single sample VCFs require temp-delete permission bug Something isn't working rare disease Change is exclusively within the scope of the rare disease pipeline
#714 opened Apr 30, 2024 by MattWellie
@MattWellie
Handle Multicohorts core Changes to the cpg-workflows api
#710 opened Apr 29, 2024 by vivbak
1
@vivbak
Ancestry Plots relies on input_datasets, which will be deprecated large cohort Change is exclusively within the scope of the large cohort pipeline
#706 opened Apr 24, 2024 by vivbak
@michael-harper
1
Cpg-utils migration hiccup core Changes to the cpg-workflows api rare disease Change is exclusively within the scope of the rare disease pipeline
#695 opened Apr 18, 2024 by MattWellie
@MattWellie
5
Wrangle list-workflows CLI arguments core Changes to the cpg-workflows api
#688 opened Apr 12, 2024 by MattWellie
1
@vivbak
Streamline usage of Dataproc? rare disease Change is exclusively within the scope of the rare disease pipeline
#666 opened Mar 27, 2024 by MattWellie
Remove/modify Query_command? core Changes to the cpg-workflows api
#647 opened Mar 14, 2024 by MattWellie
@jmarshall @vivbak @michael-harper
9
How do we notify GATK-SV stakeholders of quality failures core Changes to the cpg-workflows api rare disease Change is exclusively within the scope of the rare disease pipeline
#638 opened Mar 8, 2024 by MattWellie
@MattWellie @cassimons @EddieLF
1
GCP Housekeeping jobs? core Changes to the cpg-workflows api
#617 opened Feb 19, 2024 by MattWellie
2
Inputs.as_X methods are unintuitive core Changes to the cpg-workflows api
#611 opened Feb 6, 2024 by MattWellie
@MattWellie @vivbak @michael-harper
1
QC reporting and metadata tracking for CRAMs enhancement New feature or request
#608 opened Jan 30, 2024 by EddieLF
@cassimons @EddieLF @vivbak
Split Multiallelic Variants in main pipeline shared The change impacts both the LC and RD pipeline.
#586 opened Jan 8, 2024 by MattWellie
1
@jmarshall @MattWellie
@EddieLF @vivbak
Metamist timeouts killing pipelines core Changes to the cpg-workflows api
#585 opened Jan 5, 2024 by MattWellie
@illusional @EddieLF @vivbak
6
Check if Hap.py is working rare disease Change is exclusively within the scope of the rare disease pipeline
#482 opened Oct 5, 2023 by MattWellie
@MattWellie
Create Template Configs & Update docs to reflect changes core Changes to the cpg-workflows api
#475 opened Sep 26, 2023 by vivbak
@vivbak
1
Handle R scripts core Changes to the cpg-workflows api
#417 opened Jul 25, 2023 by vivbak
Create MD5 after finalizing CRAM alignment enhancement New feature or request
#408 opened Jul 12, 2023 by EddieLF
Analysis entries block pipeline runs core Changes to the cpg-workflows api
#390 opened Jun 27, 2023 by vivbak
2 of 3 tasks
@vivbak
1
Enable user-provided sample cohorts/datasets core Changes to the cpg-workflows api
#361 opened May 11, 2023 by MattWellie
@jmarshall @MattWellie
@cassimons @illusional
5
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