Added genotype Aligner step

Added another step in Imputation_impute2 workflow: alignWithReference.sh

Other:
* Fixed issue with additionParameters in impute2 step 
* Fixed issue with script terminating when module command didn't exist.
* Fixed relates issue with script terminating when impute2 command returned != 0 
* impute2 step know takes input from genotype aligner. This should be optional in the future.