nf-cmgg structural issues

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

14 stars 3 forks source link

issues

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Bug/sex determination

#97 nvnieuwk closed 1 month ago
1
smoove makes empty file

#96 mvheetve opened 1 month ago
1
sex unknown (ratio in gray area)

#95 mvheetve opened 1 month ago
0
Release PR 0.2.0

#94 nvnieuwk closed 1 month ago
0
Update/fix annotsv + add HPO terms

#93 nvnieuwk closed 2 months ago
1
Automatically check if the VEP cache contains a merged cache

#92 nvnieuwk opened 3 months ago
0
Make the workflow pluggable

#91 nvnieuwk closed 3 months ago
1
Make the workflow pluggable

#90 nvnieuwk closed 3 months ago
1
Fix smoove output when using `--output_callers`

#89 nvnieuwk closed 4 months ago
0
Some bugs found the output of the pipeline

#88 nvnieuwk opened 4 months ago
1
bump wisecondorx to v1.2.6

#87 nvnieuwk closed 4 months ago
0
smoove.vcf.gz indexin

#86 mvheetve closed 4 months ago
1
Add keyword shortcuts to the `--callers` parameter

#85 nvnieuwk closed 4 months ago
0
--callers all param

#84 mvheetve closed 4 months ago
3
Copy samplesheet in output directory

#83 nvnieuwk opened 4 months ago
0
Add HPO terms to the samplesheet

#82 nvnieuwk closed 2 months ago
1
Only save the last dev docs

#81 nvnieuwk closed 5 months ago
1
v0.1.0 pipeline release

#80 nvnieuwk closed 5 months ago
2
docs part 2

#79 mvheetve closed 5 months ago
0
MSG: ERROR: Cache directory vep/homo_sapiens not found

#78 mvheetve closed 5 months ago
5
Last fixes before v0.1.0 release

#77 nvnieuwk closed 5 months ago
0
docs-output

#76 mvheetve closed 5 months ago
1
Docs 0.1.0dev

#75 nvnieuwk closed 5 months ago
0
Create beautiful docs with mkdocs

#74 nvnieuwk closed 5 months ago
0
Template v2.13.1 sync + update all modules

#73 nvnieuwk closed 5 months ago
1
Add Svync standardization + other fixes

#72 nvnieuwk closed 5 months ago
1
Vcfanno annotate gene panel overlaps

#71 nvnieuwk opened 6 months ago
0
Fully support conda for all modules

#70 nvnieuwk opened 7 months ago
0
Fix annotsv TCL error

#69 nvnieuwk closed 6 months ago
2
AnnotSV issue

#68 mvheetve closed 6 months ago
2
Handling duplicate rows in samplesheet with warnings

#67 mvheetve closed 9 months ago
1
include gnomADv4 SV annotation

#66 mvheetve opened 9 months ago
0
Investigate VDS format for the creation of a false positive variants list

#65 nvnieuwk opened 9 months ago
0
Add proper testing + fix some issues found

#64 nvnieuwk closed 7 months ago
1
Better header handling

#63 nvnieuwk closed 5 months ago
0
Update tests

#62 nvnieuwk closed 5 months ago
0
Family merging

#61 nvnieuwk closed 9 months ago
1
Add VCF to JSON conversion

#60 nvnieuwk opened 9 months ago
4
Standardize variants for callers of the same type

#59 nvnieuwk closed 5 months ago
13
CNV VCFs

#58 nvnieuwk closed 9 months ago
1
Add family support

#57 nvnieuwk closed 9 months ago
1
Add BED => VCF support for CNVs

#56 nvnieuwk closed 9 months ago
1
Add filtering on annotations + fix linting

#55 nvnieuwk closed 9 months ago
2
Add comprehensive filter steps

#54 nvnieuwk closed 9 months ago
2
Investigate stranger for repeat expansion annotation

#53 nvnieuwk opened 10 months ago
0
Fix vep container issue

#52 nvnieuwk closed 9 months ago
2
Add validation

#51 nvnieuwk opened 11 months ago
1
Cnv support

#50 nvnieuwk closed 10 months ago
3
Add VCF to BEDPE conversion

#49 nvnieuwk opened 11 months ago
1
New caller: svaba

#48 nvnieuwk opened 1 year ago
0