Queue dependencies determine order of jobs
Posted in Ask the GATK team | Last updated on 2013-01-07 20:38:21

Comments (4)

I am having difficulties getting Queue to determine the order of jobs added to the queue. Using the @Input and @Output definitions of input and output files, the dependencies are defined and Queue waits for one output method to finish prior to starting the subsequent method.

Since the order the method is added to the queue does not determine the dependencies, my assumption is that Queue looks at the names of the variables added to the queue to determine which method's output is another method's input. Regardless, I've tried working with variable names in both added methods along with those defined in the @Input and @Output. All of my trials seem to come up short as Queue runs the jobs in a manner inconsistent with the @Input, @Output, and variables defined and added as arguments to methods added to the queue.

What is the secret with defining the order of jobs added to the queue? Are there any additional rules in defining variables or the @Input/@Output that I am missing?

Any help is good help. Thanks.

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