Added some global variables (picard path dir, intramate length). worked around transform to… changed the samsplit stage to use awk instead of perl. using bash cut to retrieve intramate length for R. Updated Bpipe-run command to reflect changes
Added some global variables (picard path dir, intramate length). worked around transform to… changed the samsplit stage to use awk instead of perl. using bash cut to retrieve intramate length for R. Updated Bpipe-run command to reflect changes

emilliman5/BioinfoWorkflows,emilliman5/BioinfoWorkflows,emilliman5/BioinfoWorkflows,emilliman5/BioinfoWorkflows