MOVED old testfiles to separate directory
Merge branch 'develop' into trimming
ADDED trimming skeleton
MASTER script rewrite setup
DEVELOP alternative master script to call the pipeline (in python for added flexibility)
RESTORED original path of former master script
seq-aligner Dockerfile
removed old seq-aln Dockerfile
readme
readme
readme
sv-callers dir
var-callers Dockerfile
minor edits to GATK RUNs
readme
readme
var-caller Dockerfile minor edit
ADDED trimmomatic adapter trimming (with auto PESE detection) FILTERING OPTIONS HARDCODED!!!
ADDED new master workflow (mp)
ADDED unified novoalign script (with auto PE/SE detection, illumina only)
ADDED prototype script for stampy aligner
seq-aligners Dockerfiles
var-anno v1 added Dockerfile
fix to build var-anno