I don't think this is possible, while you have an exec output plugin, it will output the same data that would be in the temp_file.
Also, not sure why you would need Logstash for that, you can output to a temp_file, have a bash script configured on your cron that would process that file and put in another directory where you would have another logstash pipeline reading it.
Depending on what your bash script will do, you may be able to do it directly on Logstash.
Please provide some more context of what you want to do with some sample data for your source and desired output.
This provides what I want to do with example.
I thought I can have the whole process with logstash without need to have some local exec running. As the data I am using will be modify and I want it to be up to date in elasticsearch