Added --header --footer --submit parameters
Removed redundant skip statement from header
Functions getFile, putFile, alloutputsexist and so are now part of the header (pbs, local)
In submit.ftl.sh scripts: # First cd to the directory with the *.sh and *.finished scripts
Merge branch 'master' of github.com:molgenis/molgenis
Merge pull request #526 from mdijkstra/master

see commit msg's