Adding the possibility of setting the cluster name

This is now defaulting to Milou.
Trying with Seq of args
Changed to correct repo in README
Merge branch 'devel' into prepareForMilou
It has to be Molmed, not molmed...
Working on getting xml setup to all workflows
Adding xml setup to all workflows
Merged exome workflows to one script
Haloplex with only aligments option
Modifying workflows and README for new apporach.
Adding test to HP for onlyAlignment
Correct md5sums and arguments for HP tests
Bold text in readme
remove typo
Resource usage names updates and HP wf updated...

... with these to control resource usage in a more fine grained way.
Removed project name reference in exome wf
Changed default nbr of threads for cuff-stuff
Updating resource usage for milou
Merge remote-tracking branch 'origin/prepareForMilou' into prepareForMilou
cohort.list instead of ${projectname}.cohort.list