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ohsu-cedar-comp-hub
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WGS-nextflow-workflow
Apache License 2.0
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calculatecontamination takes only one matched normal as input
#94
rlancaster96
opened
1 month ago
0
updates to run multiple normals as inputs to mutect2
#93
rlancaster96
closed
1 month ago
1
support for multiple normals in mutect2
#92
rlancaster96
closed
1 month ago
0
update bcftools filter command for multiple tumors
#91
rlancaster96
closed
1 month ago
1
tcga
#90
rlancaster96
closed
1 month ago
0
add sigprofiler tool
#89
rlancaster96
opened
1 month ago
1
reheader tool - echo bug
#88
rlancaster96
opened
1 month ago
0
run mutect2 on multiple tumor samples
#87
rlancaster96
closed
1 month ago
0
update documentation
#86
rlancaster96
opened
1 month ago
0
TCGA [WIP]
#85
rlancaster96
closed
1 month ago
0
add metadata from filename
#84
rlancaster96
closed
1 month ago
0
update documentation for version 0.1.0
#83
rlancaster96
closed
2 months ago
0
add funcotator annotations
#82
rlancaster96
closed
1 month ago
1
host reference files
#81
rlancaster96
closed
1 month ago
0
multiple tumor samples per patient
#80
rlancaster96
closed
1 month ago
0
multiqc report does not have sample ID information in the filename
#79
rlancaster96
opened
2 months ago
0
Multiqc samplename[WIP]
#78
rlancaster96
opened
2 months ago
0
multiple samples in input directory [WIP]
#77
rlancaster96
closed
1 month ago
0
cpu variable
#76
rlancaster96
closed
2 months ago
1
multiple sample input and variable tumor/normal name
#75
rlancaster96
closed
1 month ago
1
cpu variables
#74
rlancaster96
closed
2 months ago
0
set up nextflow linting on main branch
#73
elisabethgoldman
opened
3 months ago
1
caveman tool [WIP]
#72
rlancaster96
opened
3 months ago
0
minor cleanup
#71
rlancaster96
closed
3 months ago
0
bam to fastq
#70
rlancaster96
closed
3 months ago
1
Add MANTA to variant calling pipeline
#69
elisabethgoldman
opened
3 months ago
0
Add gridss to variant calling pipeline
#68
elisabethgoldman
opened
3 months ago
1
Add Caveman to variant calling pipeline
#67
elisabethgoldman
opened
3 months ago
1
Add BRASS to variant calling pipeline
#66
elisabethgoldman
opened
3 months ago
0
Add Strelka to variant calling pipeline
#65
elisabethgoldman
opened
3 months ago
0
Add bam to fastq to nextflow pipeline [WIP]
#64
elisabethgoldman
closed
3 months ago
0
Development
#63
rlancaster96
closed
2 months ago
0
Add additional variant filters using both FilterMutectCalls and bcftools
#62
elisabethgoldman
opened
3 months ago
1
s3 bucket compatibility
#61
rlancaster96
closed
3 months ago
1
filename convention for sampleID
#60
rlancaster96
closed
4 months ago
0
Index out of bounds error for FilterMutectCalls
#59
rlancaster96
closed
3 months ago
3
Slurm executor
#58
rlancaster96
closed
3 months ago
0
LearnReadOrientation fails on test files
#57
rlancaster96
closed
4 months ago
1
Somatic variant calling workflow
#56
rlancaster96
closed
4 months ago
2
snpEff script differs for conda vs containers
#55
rlancaster96
closed
4 months ago
1
containers in processes [WIP]
#54
rlancaster96
closed
4 months ago
1
Alignment workflow
#53
rlancaster96
closed
4 months ago
3
Alignment workflow
#52
rlancaster96
closed
4 months ago
0
Snpsift
#51
rlancaster96
closed
3 months ago
1
Issue splitting by chromosome for mutect2: "Process `mutect2` declares 5 input channels but 1 were specified"
#50
elisabethgoldman
closed
4 months ago
4
Unify mutect gatk image
#49
rlancaster96
closed
5 months ago
0
review and standardize filename formatting
#48
rlancaster96
opened
5 months ago
1
sliced fastq test files
#47
rlancaster96
closed
5 months ago
0
Added Split vcf by sample tool and workflow
#46
grie2448
closed
5 months ago
0
Multiqc dockerfile
#45
rlancaster96
closed
5 months ago
0
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