Create simple batch file and run

What is your question?

You can run FME from a batch file.

On the second line of your workbench log file (after running) is the command-line that you need.

I think you are looking for another solution.

So if you give more information on what you really want to achief we could help you solve the work easily.

I think that you could do something with the following settup:

Creator -> FeatureReader (Format: Directory and File Pathnames) -> WorkspaceRunner

Or

Creator -> FeatureReader (Format: Directory and File Pathnames) -> FeatureReader (Format: OGC GeoPackage) -> FeatureWriter (Format: Esri Geodatabase (File Geodb))

I guess you want to scan multiple folders that contain *.gpkg files and want to convert every file to a *.gdb in the same folder with the same name?

Although possible it's not often you need to use batch files with FME. Usually if you are processing lots of files you can just select them all with the reader and if they each need to go into separate output files you use a fanout on the writer and just process them all in one run.

If the workspace is more complicated and can only process on file at a time then use a master workspace with a WorkspaceRunner transformer to run the processing on each file at a time.