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umccr
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umccrise
:snake: DRAGEN Tumor/Normal workflow post-processing
https://umccr.github.io/umccrise/
MIT License
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Remove work directory
#152
pdiakumis
closed
8 months ago
0
CanRep: remove code_download from frontmatter
#153
pdiakumis
closed
8 months ago
0
CanRep: display detected viruses without integration sites
#150
pdiakumis
closed
8 months ago
0
Canrep: consider replacing DT with reactable
#149
pdiakumis
closed
8 months ago
0
Remove historical gold_standard MultiQC refdata
#147
pdiakumis
closed
1 year ago
1
oviraptor: include EBV in prioritised viruses
#146
pdiakumis
closed
1 year ago
2
Canrep: replace hypermutated field with something more intuitive
#145
pdiakumis
closed
8 months ago
1
PCGR: Switch off debug mode
#144
pdiakumis
closed
1 year ago
0
canrep: Review conda pkg list
#154
pdiakumis
closed
8 months ago
0
Oviraptor debug
#143
pdiakumis
closed
1 year ago
2
vcf2maf update
#142
pdiakumis
closed
1 year ago
0
vcf2maf: tag and release a umccr fork
#141
pdiakumis
closed
1 year ago
1
Update Cancer Gene Panel
#140
pdiakumis
closed
8 months ago
0
MultiQC: Generate background samples for DRAGEN v4
#139
pdiakumis
closed
11 months ago
1
Drop multi-gene tab from DDI table
#138
pdiakumis
closed
8 months ago
0
MultiQC: bump to v1.14+
#137
pdiakumis
closed
11 months ago
1
Multiqc error with Dragen-4 inputs
#136
skanwal
closed
11 months ago
1
Excluding stages not handled properly
#135
pdiakumis
closed
1 year ago
1
Ensembl harmonisation
#134
pdiakumis
closed
11 months ago
1
vcf2maf: hundreds of warnings for unrecognised effects
#133
pdiakumis
closed
1 year ago
0
Improve AWS CodeBuild Docker build security
#132
pdiakumis
closed
1 year ago
1
PCGR: use condarised vcf2tsvpy
#130
pdiakumis
closed
1 year ago
0
PCGR: favicon url cannot be reached
#129
pdiakumis
closed
1 year ago
0
Cacao: create separate conda env
#128
pdiakumis
closed
1 year ago
0
PCGR: annotate with REVEL/CADD/SpliceAI
#127
pdiakumis
closed
8 months ago
0
CPSR: convert predisposition genes to Ensembl Gene IDs
#126
pdiakumis
closed
8 months ago
2
PCGR: better handling of custom conda env
#125
pdiakumis
closed
1 year ago
1
Disable PCGR's MSI status
#124
pdiakumis
closed
1 year ago
1
PCGR/CPSR update
#123
pdiakumis
closed
1 year ago
4
Update ClinVar db
#122
pdiakumis
closed
11 months ago
2
Temporarily disable BPI
#121
pdiakumis
closed
1 year ago
0
Disable BPI temporarily due to timeout
#120
pdiakumis
closed
11 months ago
2
Bump oviraptor
#119
pdiakumis
closed
1 year ago
0
Legacy code cleanup
#118
pdiakumis
closed
1 year ago
0
`prep_multiqc_data` error
#117
pdiakumis
closed
2 years ago
2
Pierian/hypermutated SNV update
#116
pdiakumis
closed
2 years ago
1
Remove SV filter, bump BPI mem, add SNV counts
#115
pdiakumis
closed
2 years ago
1
SVs: do not discard BNDs with SR > PR
#114
pdiakumis
closed
2 years ago
1
Pierian SNV subsetting
#113
pdiakumis
closed
2 years ago
1
Improve Pierian input preparation
#112
pdiakumis
closed
2 years ago
5
Paranoid circos error
#111
pdiakumis
closed
8 months ago
4
Hypermutated sample fix
#110
pdiakumis
closed
2 years ago
0
Add SV Snakemake rule description
#109
pdiakumis
closed
2 years ago
2
Use biomaRt or gget for key gene table construction
#108
pdiakumis
closed
2 years ago
1
Bump BPI max mem to 30G
#107
pdiakumis
closed
2 years ago
0
SVs: rejig annotation
#106
pdiakumis
closed
8 months ago
0
Cancer report relocation
#105
pdiakumis
closed
2 years ago
0
SAGE: evaluate v3
#104
pdiakumis
closed
11 months ago
1
HMF Tools: update to 2022 versions
#103
pdiakumis
closed
11 months ago
1
Add somatic SNV Snakemake rule description
#102
pdiakumis
closed
2 years ago
6
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