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See if this works for you:
col1=$(echo $output | cut -d'|' -f5)
col2=$(echo $output | cut -d'|' -f6)
col3=$(echo $output | cut -d'|' -f7)

#!/bin/bash
IFS=" "
while read var1 var2 var3
do
echo "$var1 , $var2, $var3 "
done < "config_file"
Separating on spaces rather than commas and closing the quotes around the echoed string...