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umccr
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umccrise
:snake: DRAGEN Tumor/Normal workflow post-processing
https://umccr.github.io/umccrise/
MIT License
22
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8
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SNVs: Update CSQ metadata line based on PCGR/VEP usage
#101
pdiakumis
closed
2 years ago
0
SVs: rejig filtration
#100
pdiakumis
closed
1 year ago
0
Conda: use conda-lock for environments
#99
pdiakumis
closed
10 months ago
0
Conda: use umccr forks of conpair, pVACtools, and oviraptor
#98
pdiakumis
closed
10 months ago
1
Cancer reporter: incorporate gpgr v1.0
#97
pdiakumis
closed
2 years ago
0
Cancer reporter: use Rmd from gpgr
#96
pdiakumis
closed
2 years ago
0
Cancer reporter: incorporate sigrap
#95
pdiakumis
closed
2 years ago
0
CPSR: update to v1
#94
pdiakumis
closed
1 year ago
0
PCGR: update to v1
#93
pdiakumis
closed
1 year ago
1
Cancer reporter: add SNV filtration summary tables
#92
pdiakumis
closed
2 years ago
1
Improve hypermutated sample SNV filtering
#91
pdiakumis
closed
2 years ago
0
Compress intermediate files
#90
pdiakumis
closed
1 year ago
1
SNVs not filtered as expected on ICA
#89
pdiakumis
closed
2 years ago
1
BPI (break-point-inspector) OutOfMemoryError
#88
pdiakumis
closed
2 years ago
5
Minor DRAGEN MultiQC updates
#87
scwatts
closed
2 years ago
0
Pin pandoc and update MultiQC
#86
pdiakumis
closed
2 years ago
3
Package `multiqc-1.10dev+umccrise_bcbio_aws.0.0.1-py_0` requires python >=3.6,3.9
#85
pdiakumis
closed
2 years ago
1
pandoc document conversion failed with error 25
#84
pdiakumis
closed
2 years ago
3
Handle multiple '@RG SM' BAM header fields
#83
scwatts
closed
2 years ago
0
MultiQC tidy JSON output to Parquet
#82
brainstorm
closed
2 years ago
1
Update HISTORY for 2.0.0
#81
scwatts
closed
2 years ago
0
Remove bcbio test from the CodeBuild build process
#80
scwatts
closed
2 years ago
0
Add DRAGEN germline fragment length QC file
#79
scwatts
closed
2 years ago
0
Fix DRAGEN file discovery and PCGR install
#78
scwatts
closed
2 years ago
0
Use Ubuntu base Docker image from public ECR
#77
scwatts
closed
3 years ago
0
Update HISTORY for 1.2.4
#76
pdiakumis
closed
3 years ago
0
Apply fixes for AWS/bcbio
#75
scwatts
closed
3 years ago
2
Update to handle DRAGEN data
#74
scwatts
closed
3 years ago
3
Handle missing PURPLE rainfall plot
#73
pdiakumis
closed
3 years ago
2
PURPLE: handle missing rainfall plot when > 100K SNVs
#72
pdiakumis
closed
3 years ago
0
vcf2maf: ignore "Use of uninitialized value" warnings (fixes #61)
#71
pdiakumis
closed
3 years ago
1
cancer report: include DBS signatures (fixes #59)
#70
pdiakumis
closed
3 years ago
0
cancer report: render even with error; standardise example data paths
#69
pdiakumis
closed
3 years ago
0
Update Dockerfile and install.sh
#68
scwatts
closed
3 years ago
1
CONDA_PREFIX set to `//miniconda/envs/` in Dockerfile because root user has no HOME
#67
alexiswl
closed
3 years ago
7
Update Conda environments: pin package versions, use `umccr` channel, bump NGS Utils version
#66
scwatts
closed
3 years ago
2
Compress multiqc_data.json
#65
brainstorm
closed
3 years ago
3
Ship derived tool logs to CloudWatch instead of the local instance
#64
brainstorm
closed
3 years ago
1
Fix unsafe YAML Loader
#63
brainstorm
closed
3 years ago
1
Fix AWS documentation
#62
brainstorm
closed
3 years ago
1
Fix vcf2maf warnings
#61
brainstorm
closed
3 years ago
3
Missed bcbio qc metrics
#60
ohofmann
closed
3 years ago
10
MutationalPatterns: handle dbs context error
#59
pdiakumis
closed
3 years ago
1
Pierian: rename PURPLE minorAlleleCopyNumber column to minorAllelePloidy
#58
pdiakumis
closed
3 years ago
0
cancer report: fix oncoviruses stage
#56
pdiakumis
closed
3 years ago
1
Drop signatures attributed to sequencing artefacts
#57
pdiakumis
closed
3 years ago
0
Updated base ubuntu image to use ECR
#55
victorskl
closed
3 years ago
1
Pinned dvc version in CodeBuild build image
#54
victorskl
closed
3 years ago
0
Update hmf conda env
#53
pdiakumis
closed
4 years ago
0
Cancer report cleanup
#52
pdiakumis
closed
4 years ago
1
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