I have two files with single fields. It looks like:
File A File B a1 b1 a2 b2 a3 b3 a4 b4
I would like to have a1,b1; a2,b2 but when I connect two inputs into transformation Kettle says that inputs have different layouts
You don't have any details of your transformation, but I guess you picked the 'Append streams' step. You should use the Merge Join step and two 'Add sequence' step to add a line nr to the input (set a different counter name for both steps). Connect your two 'Add sequence' steps to this 'Merge Join' step configure the key fields as line number and set the join type to: 'FULL OUTER'. Next you can use a Select values step to get rid of the line number columns.