Unfortunately, CloverETL does not support emojis by default. No CTL function can help you directly with emojis. Also, I am not sure how the emojis are represented in your files, what encoding is used etc.
1) Do you have any sample file containing emojis, please? Could you post it here or send via email?
2) How big your input files are?
3) Do the input files contain just text or also some structured data?
4) Are they binary files or plain text files?
There is a java library
that could be useful if you decide to write your own java transformation.
You can also use find function of CTL and look for regular expressions