Beri

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

I don't think there would be an easy way in WDL to reorganize the flattened array into a object[String, Array[Files]]. If there is, the best place to find it is in the WDL specification.  I'm not c...

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• Edited October 27, 2020 19:37
• 1 vote

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3. Hail notebook error: Consider boosting spark.yarn.executor.memoryOverhead

Hi Elizabeth, What container are you using?You probably won't be able to edit the default docker containers but perhaps you can create a custom container based on the defaults and add the required ...

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• November 21, 2019 17:25
• 1 vote

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2. General Discussion
3. Updating Hail

Hi Tim, We're hoping to have a Hail docker image as one of the available environments on the UI soon, and it will feature the newest Hail. At this time there is no way for users to upgrade their ow...

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• November 05, 2019 16:20
• 1 vote

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2. General Discussion
3. SortAndFixTags FileTruncatedException error

The error you've listed isn't originating for Terra/Firecloud, its a message coming from the GATK tool, you'll be less likely to find tool errors on this forum. Instead you could try looking for er...

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• Edited June 29, 2019 21:50
• 1 vote

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2. General Discussion
3. combine outputs

It's not related to the CombineVariants task but to your workflow as a whole. Your workflow is expecting and array of files as input but when you select Samples as the "root entity" your telling Te...

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• June 26, 2019 18:52
• 1 vote

1. Community
2. Featured Workspace Help
3. CNN configs need outputs

Hi Laura,  Thanks for the feedback, I'll double check that the rest of the gatk featured workspaces have at least their main output configs set for the workflows. 

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• May 17, 2021 19:56
• 0 votes

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2. Featured Workspace Help
3. Large WGS cohort genotyping with 'GATK Best Practices Germline SNPs and INDELS'

The workflow authors suggested if you are planning to work with a large sample set then try to enabling GnarlyGenotyper instead of GenotypeGVCFs in the workflow. This would require reblocking the g...

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• Edited February 17, 2021 15:07
• 0 votes

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2. Featured Workspace Help
3. Large WGS cohort genotyping with 'GATK Best Practices Germline SNPs and INDELS'

Hi dsilencio, I've forwarded your question to the workflow authors and we'll get back to you with an answer.

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• February 03, 2021 15:08
• 0 votes

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2. Featured Workspace Help
3. how to run latest GATK Best Practices workflows

Hi Ashish Agarwal The easiest place you can access the latest implementation GATK's Best Practices workflows to be run on Terra is GATK Best Practices Workflows collection in Dockstore. Currently t...

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• Edited August 27, 2020 15:12
• 0 votes

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2. Featured Workspace Help
3. gatk4-exome-analysis-pipeline BamProcessing.SortSam fails with Error Code 10

I'm happy to hear that you were able to resolve the issue and thanks for posting the steps used to resolve it. Regarding relative imports, this is a feature offered by Dockstore and isn't available...

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• June 08, 2020 14:03
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