Assemble jobs into sub-folders

[netaware]

Hello,
I have to create a flow that will compare 2 text files with BC4. They have slightly different names. I want to assemble the job with one file in a BEFORE directory and one file in an AFTER directory. Then I can run a script to compare them.
I do not want to rename the files because I want the log file, that is created, to have the real filenames in it.
How can I assemble a job with sub-directories?

Example:
XXXYYY
Before
XXXYYY1.txt
After
XXXYYY2.txt

[freddyp]

Assemble the files into a folder separately and then assemble the two folders.

[netaware]

Thank you for your help !