Giulio Genovese

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3. map Array[File] to Object[samplename, Array[Files] based on filename

The appropriate way to group/aggregate elements of an array is to use the collect_by_key() function although this is only available in WDL development version. As an example, the following WDL: ver...

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• December 23, 2020 16:40
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3. cromwell file permission declined

I think the problem is simply that in the code: python /usr/local/bin/sample_sheet \ "${inputFile}" You left a space after the "\" character, so it is not interpreted as a line continuation.

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• September 27, 2020 16:08
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3. Job seems stuck indefinitely at the delete intermediate files step and does not complete

Super! That's awesome and very timing. Thank you Jason! :-)

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• August 19, 2020 21:48
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2. Completed Feature Requests
3. Support workflows with more than 50,000 nodes

I looked at the code and the error is generated from the ScatterKey.scala file: if(scatterSize > maxScatterWidth) { workflowExecutionActor ! JobFailedNonRetryableResponse(this, new Exception(s"Wor...

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• August 12, 2020 22:58
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1. Community
2. Completed Feature Requests
3. Support workflows with more than 50,000 nodes

A job I submitted yesterday on Terra failed with the following message: Workflow has scatter width 38717, which is more than the max scatter width 35000 allowed per scatter! The scatter was not ca...

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• August 12, 2020 14:18
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3. unable to view status of running job

Just wanted to bring some closure. Rewriting the WDL to minimize the amount of metadata passed to tasks by passing files rather then Array[String] objects whenever possible did the trick and I was ...

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• July 25, 2020 03:31
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3. Job seems stuck indefinitely at the delete intermediate files step and does not complete

Okay! There is no immediate hurry on my side. I am very happy to know that a solution is in the making. I know I am pushing the limits of Terra a bit, but overall I have been very positively impres...

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• July 25, 2020 02:22
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3. Terra fails to delocalize files listed through read_lines()

As it is relevant to this post, I will mention that another possible solution to requiring that the list of output files be computed ahead of the task starting is to have the suffix() function impl...

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• July 25, 2020 01:49
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3. Job seems stuck indefinitely at the delete intermediate files step and does not complete

Thank you Khalid. I am fine for this particular workflow. I wrote the WDL and I know exactly what it does so I know how to handle this. I am more worried about this happening to other users that wi...

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• July 24, 2020 23:39
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3. Job seems stuck indefinitely at the delete intermediate files step and does not complete

It looks like someone did something ... the job used to say "Started Jul 22, 1:20 AM" and now it says "Started: Today, 5:33 PM" and "Ended: Today, 5:34 PM (0h 0m)": And it claims to have failed wh...

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• July 24, 2020 22:27
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