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nf-cmgg
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germline
A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data
https://nf-cmgg.github.io/germline/
MIT License
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Allow runs until genomicsdb, get regions from GVCF for joint-genotyping
#137
nvnieuwk
closed
1 year ago
1
Remove the need to supply a CRAM file when a GVCF is supplied
#136
nvnieuwk
closed
1 year ago
1
Update merging of crams + some other issues
#135
nvnieuwk
closed
1 year ago
1
Improve efficiency of CRAM merging
#134
nvnieuwk
closed
1 year ago
1
Optimize resources for `SAMTOOLS_MERGE`
#133
nvnieuwk
closed
1 year ago
1
Output samplesheet by default
#132
nvnieuwk
closed
1 year ago
1
Add only_call mode
#131
nvnieuwk
closed
1 year ago
1
Make it possible to only get gvcfs
#130
nvnieuwk
closed
1 year ago
0
Release 1.2.2
#129
nvnieuwk
closed
1 year ago
1
Update output dir
#128
nvnieuwk
closed
1 year ago
1
Investigate non-coding variants annotation
#127
nvnieuwk
opened
1 year ago
0
Investigate UTRannotator VEP plugin
#126
nvnieuwk
opened
1 year ago
0
Release PR v1.2.1
#125
nvnieuwk
closed
1 year ago
1
Update docs for release 1.2.1
#124
nvnieuwk
closed
1 year ago
1
Don't scatter genomicsdb
#123
nvnieuwk
closed
1 year ago
1
Investigate perbase merge_adjacent
#122
nvnieuwk
opened
1 year ago
0
Add VEP nf-core subwf for better scattering
#121
nvnieuwk
closed
1 year ago
1
Fix validation bed file
#120
nvnieuwk
closed
1 year ago
1
Deepvariant
#119
nvnieuwk
closed
11 months ago
2
add dragen_mode option
#118
nvnieuwk
closed
1 year ago
1
Add deepvariant
#117
nvnieuwk
closed
1 year ago
2
Fix validation
#116
nvnieuwk
closed
1 year ago
1
Convert GVCF to VCF before validating
#115
nvnieuwk
closed
1 year ago
1
Add nf validation support + fix bedtools jaccard
#114
nvnieuwk
closed
1 year ago
1
Bedtools Jaccard issue
#113
nvnieuwk
closed
1 year ago
0
Release PR v1.2.0
#112
nvnieuwk
closed
1 year ago
1
Template merge v2.8
#111
nvnieuwk
closed
1 year ago
1
Release PR v1.2.0
#110
nvnieuwk
closed
1 year ago
2
Update docs
#109
nvnieuwk
closed
1 year ago
1
Update metro map and add better docs
#108
nvnieuwk
closed
1 year ago
5
Add jaccard to validation
#107
nvnieuwk
closed
1 year ago
1
Add dockerfile
#106
nvnieuwk
closed
1 year ago
1
Update efficiency of the pipeline
#105
nvnieuwk
closed
1 year ago
2
Don't merge callable BED files if multiple CRAMs were given, rather remake them with mosdepth
#104
nvnieuwk
closed
1 year ago
2
Add a flag to make it possible to run a more in-depth run of mosdepth
#103
nvnieuwk
closed
1 year ago
1
Lower the label of genotypegvcfs
#102
nvnieuwk
closed
1 year ago
1
Adjust the scatter count in genotyping dependent on the family size
#101
nvnieuwk
closed
1 year ago
1
Change the way callable BED works + genotyping fixes + ped fix
#100
nvnieuwk
closed
1 year ago
4
Update no dragstrmodel run
#99
nvnieuwk
closed
1 year ago
0
Add dockerfile
#98
matthdsm
closed
1 year ago
5
hotfix for validation
#97
nvnieuwk
closed
1 year ago
1
Add gvcf input
#96
nvnieuwk
closed
1 year ago
1
Make `--genotype false` do what it's supposed to do
#95
nvnieuwk
closed
1 year ago
1
Remove non coverage regions from BED files
#94
nvnieuwk
closed
1 year ago
1
Add truth bed for validation
#93
nvnieuwk
closed
1 year ago
1
Add back ROI support and uniformize all scattering
#92
nvnieuwk
closed
1 year ago
3
Add better code comments
#91
nvnieuwk
closed
1 year ago
2
Release 1.1.2
#90
nvnieuwk
closed
1 year ago
1
Add param for scatter threshold
#89
nvnieuwk
closed
1 year ago
1
Release v1.1.1
#88
nvnieuwk
closed
1 year ago
0
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