script properties#

Nearly all modules are "script modules". The module writes one or more scripts to divide the work load, and each script is run
on an independent cluster node (if pipeline.env=cluster), or
on an independent aws node (if pipeline.env=aws), or
one at a time on the current machine (if pipeline.env=local).

Property	Description
script.defaultHeader	string Store default script header for MAIN script and locally run WORKER scripts. default: #!/bin/bash
script.fileRefreshDelay	integer delay this many seconds after scripts complete to allow the file system to reflect changes from a worker node/container/virtual machine. default: 1
script.numThreads	integer Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter. default: 8
script.numWorkers	integer Set number of samples to process per script (if parallel processing) default: 1
script.permissions	string Used as chmod permission parameter (ex: 774) default: 770
script.timeout	integer Sets # of minutes before worker scripts times out. default: null

All script modules have a "script" subdirectory.

There is one "MAIN" script for the module, which launches the worker scripts. Each worker script does the work for one batch; a set of samples.