See comments

Fixes:

1. The part of the bash script that estimates the time passed had a serious bug. The expression: ((a=b)) as a command exits with '1' sometimes. Check:
#> ((abc=0))
#> echo $?
1

Given that we have "set -e" at the beginning that was a fatal error. Exiting at that point didn't allow the footer part of the script to run, which means that the .env files were not saved and the workflow stopped at that point.

2. The impute2SamplesMerged and impute2SamplesMergedInfo variables returned ALL the values from previous runs to the concatResSamples script. So I had to put an iterator to take only the values of this chunk.  

3. Corrected liftover script to save output in bed,bim,fam