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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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add nft-bam to germline
#179
nvnieuwk
closed
1 month ago
0
Template v2.14.1
#178
nvnieuwk
closed
1 month ago
0
v1.6.0 release PR
#177
nvnieuwk
closed
2 months ago
1
Fix multiqc reports
#176
nvnieuwk
closed
2 months ago
0
Feature: pluggable workflow
#175
nvnieuwk
closed
2 months ago
1
Migrate to nf schema
#174
nvnieuwk
closed
2 months ago
2
Fix updio join
#173
nvnieuwk
closed
3 months ago
0
Multi family support in UPDio
#172
nvnieuwk
closed
3 months ago
2
Add automap
#171
nvnieuwk
closed
3 months ago
1
Update docs + add mkdocs for pretty docs
#170
nvnieuwk
closed
3 months ago
0
Rework nf-test
#169
nvnieuwk
closed
3 months ago
0
Add support for bigger families in UPDio
#168
nvnieuwk
closed
3 months ago
1
Add UPDio to the pipeline
#167
nvnieuwk
closed
3 months ago
0
Explore `VariantRecalibrator` and `ApplyVQSR` for better filtering
#166
nvnieuwk
opened
4 months ago
2
Release PR v1.5.1
#165
nvnieuwk
closed
4 months ago
1
Release v1.5.0
#164
nvnieuwk
closed
4 months ago
0
v1.4.2 - Path release ensembl vep
#163
nvnieuwk
closed
5 months ago
2
Save a process, create index within the module
#162
matthdsm
closed
5 months ago
2
Add `vcf_check` as a safety guard
#161
nvnieuwk
closed
3 months ago
1
Release PR v1.4.1
#160
nvnieuwk
closed
6 months ago
1
Fix concat issues
#159
nvnieuwk
closed
6 months ago
1
Some additional filter improvements
#158
nvnieuwk
closed
7 months ago
1
Add alphamissense VEP plugin
#157
nvnieuwk
closed
7 months ago
1
update profiles seqplorer, hypercap and seqcap
#156
nvnieuwk
closed
7 months ago
1
Release PR v1.4.0
#155
nvnieuwk
closed
7 months ago
1
Update all modules to the latest version
#154
nvnieuwk
closed
7 months ago
1
Update docs for 1.4.0 release
#153
nvnieuwk
closed
7 months ago
1
Update vep handling
#152
nvnieuwk
closed
7 months ago
1
Feat/sample specific vardict options
#151
nvnieuwk
closed
8 months ago
1
Decompose, normalization and specific profiles
#150
nvnieuwk
closed
9 months ago
1
Make Vardict min AF variable per sample
#149
nvnieuwk
closed
5 months ago
1
Template v2.10
#148
nvnieuwk
closed
9 months ago
1
Create profiles for different analysis
#147
nvnieuwk
closed
9 months ago
1
Add downloading of the VEP cache when not given
#146
nvnieuwk
closed
5 months ago
1
Use contigs BED file for genomicsdb
#145
nvnieuwk
closed
9 months ago
2
Major refactor + add Vardict caller
#144
nvnieuwk
closed
9 months ago
1
Add normalization and decomposing to VCF2DB
#143
nvnieuwk
closed
9 months ago
4
Update coverage_fast parameter
#142
nvnieuwk
closed
9 months ago
1
Add somatic calling
#141
nvnieuwk
opened
1 year ago
0
Add VarDict calling
#140
nvnieuwk
closed
9 months ago
5
Increase default memory in some processes
#139
nvnieuwk
opened
1 year ago
0
Release v1.3.0
#138
nvnieuwk
closed
1 year ago
1
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
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