So far just the qc but pushing for quick test
forgot to do compile check
debugging
value interpreted as global fixed
Added timing outputs, run and then test script by hand
Cleaner outputs for timing
Timing and QC metrics, ready for testing in pulldown, of okay then attempt genome
Tiny change to data structure
Had to rework some stuff for timing code to work correctly
Missing memory set for job, also simplified dependencies.
debug
Remove debug and correct pathing to getTbi.pl
Mac line feeds introduced in pl #! by netbeans perl plugin
Force change from Mac line feed to unix
Linefeeds really messed up, fixed
No newline at end to json files, technically not a valid text file without
copied updated vcf upload and updated versions in readme
ASCAT now doesn't need a defined loci to determine gender for GRCh37d5 (hs37d5)
Update install order
Builds all code for CGP pipeline, provided apt-get items detailed in README are installed