refactored runJob and RunJob to fix state bug
refactored runJob and RunJob to fix state bug

ohsu-comp-bio/funnel,ohsu-comp-bio/funnel,ohsu-comp-bio/funnel,buchanae/funnel,buchanae/funnel,adamstruck/funnel,adamstruck/funnel,buchanae/funnel,adamstruck/funnel,ohsu-comp-bio/funnel,adamstruck/funnel,buchanae/funnel