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nf-cmgg
/
structural
A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads
https://nf-cmgg.github.io/structural/
MIT License
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New caller: svaba
#48
nvnieuwk
opened
1 year ago
0
Expansionhunter
#47
nvnieuwk
closed
11 months ago
3
Genotyping update
#46
nvnieuwk
closed
1 year ago
3
Add expansionhunter
#45
nvnieuwk
closed
1 year ago
1
tune SVcaller parameters
#44
nvnieuwk
opened
1 year ago
0
make testprofile document
#43
nvnieuwk
closed
10 months ago
0
Template merge v2.8
#42
nvnieuwk
closed
1 year ago
2
Add expansionhunter for detection of repeats
#41
nvnieuwk
closed
11 months ago
1
Merge wrongly placed commits
#40
nvnieuwk
closed
1 year ago
1
re-add gridss support
#39
nvnieuwk
opened
1 year ago
1
Fix `manta` errors
#38
nvnieuwk
closed
11 months ago
1
Fully document the pipeline
#37
nvnieuwk
closed
5 months ago
1
Add MEI support
#36
nvnieuwk
opened
1 year ago
3
Fully implement annotation
#35
nvnieuwk
closed
1 year ago
5
Fully add annotation
#34
nvnieuwk
closed
1 year ago
1
fix smoove output
#33
nvnieuwk
closed
1 year ago
1
Fix smoove output
#32
nvnieuwk
closed
1 year ago
1
Add bcftools sort
#31
nvnieuwk
closed
1 year ago
1
edit PosCon3 samplesheet_big.csv
#30
mvheetve
closed
1 year ago
1
Add annotation + viola + join checks + cleanup
#29
nvnieuwk
closed
1 year ago
1
viola + join checks
#28
nvnieuwk
closed
1 year ago
2
Investigate the use of Viola-SV
#27
nvnieuwk
closed
1 year ago
0
Add genotyping
#26
nvnieuwk
closed
1 year ago
8
Add gridss
#25
nvnieuwk
closed
1 year ago
2
Refactor the pipeline to prepare for subworkflow export to nf-core
#24
nvnieuwk
closed
1 year ago
2
Add smoove & tests
#23
nvnieuwk
closed
1 year ago
2
hotfix dev test
#22
nvnieuwk
closed
1 year ago
0
New series of fixes and features
#21
nvnieuwk
closed
1 year ago
1
Refactoring
#20
nvnieuwk
closed
1 year ago
0
Continue module gather batch evidence
#19
nvnieuwk
closed
1 year ago
1
Add MakeCohortVCF subworkflow
#18
nvnieuwk
closed
1 year ago
0
Add GenotypeBatch subworkflow
#17
nvnieuwk
closed
1 year ago
0
Add MergeBatchSites subworkflow
#16
nvnieuwk
closed
1 year ago
0
Add FilterBatch subworkflow
#15
nvnieuwk
closed
1 year ago
0
Add GenerateBatchMetrics subworkflow
#14
nvnieuwk
closed
1 year ago
0
Add ClusterBatch subworkflow
#13
nvnieuwk
closed
1 year ago
0
Add CNV support
#12
nvnieuwk
closed
10 months ago
5
Finish GATHER_BATCH_EVIDENCE
#11
nvnieuwk
closed
1 year ago
0
Fix EVIDENCE_QC
#10
nvnieuwk
closed
1 year ago
0
Finish Scramble
#9
nvnieuwk
opened
1 year ago
1
Reheader the Whamg VCFs
#8
nvnieuwk
closed
1 year ago
0
Fix `MAKE_BINCOV_MATRIX`
#7
nvnieuwk
closed
1 year ago
0
added positive control test cases in /testdata and to the samplesheet
#6
mvheetve
closed
1 year ago
1
Module gather batch evidence
#4
nvnieuwk
closed
1 year ago
0
Module evidence qc
#3
nvnieuwk
closed
1 year ago
0
Birth of a pipeline
#2
nvnieuwk
closed
2 years ago
3
use this repo
#1
matthdsm
closed
1 year ago
0
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