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nf-cmgg
/
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
6
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1
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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
Add truth_bed option to samplesheet
#87
nvnieuwk
closed
1 year ago
1
Fix the scatter issue (and some other small fixes)
#86
nvnieuwk
closed
1 year ago
1
Scattering not working as it's supposed to
#85
nvnieuwk
closed
1 year ago
1
Add file check for SDF folder
#84
nvnieuwk
closed
1 year ago
6
Release PR v1.1.0
#83
nvnieuwk
closed
1 year ago
1
Final fixes and doc updates
#82
nvnieuwk
closed
1 year ago
1
Update scatter + fix join mismatches
#81
nvnieuwk
closed
1 year ago
1
Update scatter
#80
nvnieuwk
closed
1 year ago
1
Don't run the somalier subworkflow for single sample families
#79
nvnieuwk
closed
1 year ago
1
⚠️ Fix all join mismatches!
#78
nvnieuwk
closed
1 year ago
1
Give gatk4 some mem margin for docker
#77
matthdsm
closed
1 year ago
3
Possible improvement to vep
#76
matthdsm
closed
1 year ago
7
Re-add ROI support for WES
#75
nvnieuwk
closed
1 year ago
4
catch gatk OOM exit code
#74
matthdsm
closed
1 year ago
2
Feat/deprovision haplotyper
#73
matthdsm
closed
1 year ago
1
Add regions to scatter filenames
#72
nvnieuwk
closed
1 year ago
1
validation: Investigate bedtools jaccard
#71
matthdsm
closed
1 year ago
4
Add sanity check for `join` operations
#70
matthdsm
closed
1 year ago
3
fix base process selectors for in house cluster
#69
matthdsm
closed
1 year ago
2
Standardize resource request to 8c/64gb
#68
matthdsm
closed
1 year ago
3
Haplotypecaller is overprovisioned
#67
matthdsm
closed
1 year ago
2
Don't overwrite multiqc in the outdir
#66
nvnieuwk
closed
1 year ago
4
Add automated lookup of individuals VCFs in the output folder
#65
nvnieuwk
closed
1 year ago
4
Improve PED generation with somalier
#64
nvnieuwk
closed
1 year ago
1
Add validation subwf
#63
nvnieuwk
closed
1 year ago
2
fix for genomicsdbimport
#62
nvnieuwk
closed
1 year ago
1
Improve scatter efficiency
#61
nvnieuwk
closed
1 year ago
1
Improve scattering even more
#60
nvnieuwk
closed
1 year ago
6
metro map svg
#59
nvnieuwk
closed
1 year ago
0
add support for ROI and callable beds
#58
nvnieuwk
closed
1 year ago
1
Add an option to supply a samplesheet with called GVCFs to directly start genotyping
#57
nvnieuwk
closed
1 year ago
1
Processify everything
#56
nvnieuwk
closed
1 year ago
1
Add ROI bed and callable region inputs to samplesheet instead of single BED
#55
nvnieuwk
closed
1 year ago
0
Fix automatic dbsnp index creation not working
#54
nvnieuwk
closed
1 year ago
1
Fix PED error
#53
nvnieuwk
closed
1 year ago
1
Convert the scattering and header merging to processes
#52
nvnieuwk
closed
1 year ago
3
Improve `bed_scatter_groovy` to use less memory
#51
nvnieuwk
closed
1 year ago
0
improved the automatic bed generation
#50
nvnieuwk
closed
1 year ago
1
Fix ped merge
#49
nvnieuwk
closed
1 year ago
0
fix ped merging
#48
nvnieuwk
closed
1 year ago
1
Add "validation" subworkflow
#47
matthdsm
closed
1 year ago
5
Update samplesheets
#46
nvnieuwk
closed
1 year ago
0
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