Jason Cerrato

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3. How do I pass an array(array(file)) to another task?

Hi Aisling, I think this is a fantastic idea. I'm not aware of any documents that outline the differences between working with Terra Cromwell vs local Cromwell, but I think its value is highly appa...

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• November 17, 2021 21:55
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3. How do I pass an array(array(file)) to another task?

Hi Aisling, Thinking through the WDL side of the situation, it may be reasonable that the WDL spec does not have information about delocalizing nested arrays, as delocalization is a concept specifi...

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• November 16, 2021 15:45
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3. How do I pass an array(array(file)) to another task?

Hi Aisling, No problem at all! I will discuss this with the engineer to see if this test is something they can set up in the near future. I'll also verify that this information doesn't exist in the...

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• November 16, 2021 15:35
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3. Cannot open Job Manager: 403 Forbidden

Hi jtsuji, This issue has been resolved and you should be able to access Job Manager at this time. If you run into any trouble, please let us know! Kind regards, Jason

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• November 10, 2021 16:16
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3. How do I pass an array(array(file)) to another task?

Hey Aisling, Just wanted to follow up here to see if there was anything we can do to further assist here. If you have any questions, please let us know! Kind regards, Jason

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• November 09, 2021 21:06
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3. How do I pass an array(array(file)) to another task?

Hey Aisling, Thanks for providing us with that information. A member of our Batch team took a closer look and it seems that Cromwell doesn’t currently support delocalizing files in nested arrays. I...

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• November 05, 2021 20:35
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3. Unable to determine reason for Mutect2 failure in Terra from log file

Hi Elise, Thanks for following up. It looks like this question is more about the functionality of the Funcotator tool, which would be better suited for the GATK Support team. I'd highly recommend b...

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• November 02, 2021 15:24
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3. output files hidden in glob-* directories

Hi Stephanie, Thanks for writing in. This is a great question! This ultimately boils down to what your end goals are and what works best for your process. For most, writing outputs back to their da...

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• October 29, 2021 14:59
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3. Unable to determine reason for Mutect2 failure in Terra from log file

Hi Elise, I've walked through this WDL with a colleague and found that there is a way to increase memory for the Funcotate task, in something of a roundabout fashion. The Funcotate task's memory is...

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• October 28, 2021 20:45
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3. Unable to determine reason for Mutect2 failure in Terra from log file

Hey Elise, I agree that the WDL is written in such a way that the defaults can't be overwritten by the input variables. I'm going to try and track down whether this is a known issue with the WDL an...

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• October 28, 2021 20:27
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