CHNAGED file permissions
STARTED writing molpath (ruffus based pipeline)
MOVED classic molpath (python+bash)
Merge branch 'ngsmaster' into molpath
finished ruffus pipeline template
ADDED new NGSjob class for the revised config files
Merge branch 'dev' into jobfile
RENAMED molpath to ngsEasy
GENERIC sample parser
SPLIT configuration file (ngs,pipeline)
ADDED readme
ADDED sample configuations
CLEANUP
CHANGED universal configfile parser
BUGFIXES in ngsEasy.py and NGSjob.py
FINISHED a lot of stuff
TESTING PENDING
Merge branch 'jobfile' into molpath
CHANGED bam indexing flow
ADDED target and forced task command line option
CHANGED mutiple input pipeline tasks to use @collate
MINOR changed logger
ADDED mpileup variant calling
CHANGED naming of intermediary files
ADDED FastQ pair check (first and last read)
Merge branch 'cmdparse' into molpath
ADDED caller dependent variant filtering
MOVED python/ruffus pipeline
WiP
LOTS OF PROGRESS (vcf handling, merging, annotating..)
ADDED nonGATK merging script (uses gatk switch)
ADDED docker configuration group in config file
ADDED mergevcf minial evidence parameter and resolving of incompatible variants
BUGFIX mergevcf
ADDED timejob decorator (logs function runtime)