LOGAN development version

Changed over to Nextflow CCBR template and pip packaging
- Processes moved to modules/local directory
- Workflows under the subworkflows/local directory
- 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