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Workbench uses thread and Timer.scheduleAtFixedRate method to trigger the daily and weekly report. Time for execution is kept constant. It works like a scheduler.
As Pravin mentions, the checking of those boxes in Workbench triggers scheduled jobs within the EAC that kicks off the scripts at the appropriate time/day. But as you've noticed, there's not a ton of flexibility and you don't get cron or Windows Scheduler-type capabilities.
If you need to do something special, you can manually kick off the report generation scripts from your control directory using the runcommand.bat (or sh) script or place the command into a cron/Windows Scheduler job:
For example, to kick off the WeeklyReports job, you would do this:
runcommand.sh WeeklyReports runSo, assuming you go down the route of creating multiple ReportGenerators and scripts, you would create a job to kick off the new script you've created at the appropriate time.
Hope that helps,