added manual run submit script
added another option to manual submit to allow us to skip the realignment check
Merge branch 'master' of ssh://github.com/kellrott/tcga_realign into dev_cwilks1
will automatically detect realignment check failure and upload to PCAWG_CHECK
added the actual template file
fixed bug where timing, qc, and merge stats werent getting picked up
Merge pull request #16 from kellrott/dev_cwilks1

Dev cwilks1