If you receive logfiles in batches, you can use the batch input to consume logs and then delete them. This should only be used against a copy of the logs.
See the following example:
[batch:///var/batch/logs/*/access.log*] sourcetype=access host_segment=4 move_policy = sinkhole
This stanza would index the files in the given directory and then delete the files. Make sure this is what you want to do!