Use Directory and File Pathnames Reader pointed at the folder containing your Collada files. In Parameters set Path filter to *.dae and Recurse into Subfolders to Yes (if needed).

Use FeatureReader with Format set to Collada, Dataset set to the path_windows (or path_unix) attribute AND Accumulation Mode set to Merge Initiator and Result (this is important if you want to preserve the filenames). Attributes will need to be exposed manually or imported via some features.

Make your regular transformation and in the CityGML writer enable Fanout Dataset and in Fanout Expression give a name to your files (extension included) (you can even use the path_filename attribute from PATH Reader plus the .gml/.xml/.gz extension).

Thank you for the reply! I will follow your instructions and keep you updated on the progress.

Hello @caracadrian ! I followed your instructions and even added path reader and set fanout expression to @Value(path_filename).gml but I only get one file as the output. Do you think I'm missing something?

It'll be easier if you post a screen shot of your workflow (ideally with summary annotation on for each transformer) or upload the workspace here as an attachment.