- Added additional SV callers(GRIDSS) and annotation for SV (GRIPSS) + CNV Callers (ASCAT, CNVKit) + SNV (#66Deepsomatic)
- Adds ffpe filtering #67
- Bugfixes for hg19 by fixing references
- Updated PON for hg38 using TCGA/GDC references #59
- In development: adding exome support by using bed file to restrict calling regions
- Refactored modules to be similar to nf-core
- Fix error in varscan #71
- Created separate docker #63
- Changed over to Nextflow CCBR template and pip packaging
- Processes moved to
modules/localdirectory - Workflows under the
subworkflows/localdirectory - Processes fall under low/med/high, but added a somaticvariant caller process
- Built AnnotSV/ClassifyCNV container (#40)
- Converts strelka to add GT/AD column for downstream annotaiton (#55)
- Adds hg19 genome build for for purple (#54)
- Keeps VCF sample format as Tumor,Normal (#58)
- Updated Docker base image to GATK 4.6, Adds cyvcf2 (for #54) Somalier 0.2.19, Muse 2.0.4 and HMFtools amber, purple, sage
- Processes moved to