Beri

Hide workflow submission in Job History

This is mainly regarding publishing a workspace with failed submissions The first draft of a workspace normally has a few runs with failed attempts before succeeding. Failed submissions clutter the...

• Beri
• March 11, 2022 12:57
• 2 followers
• 1 comment
• 0 votes

Adding my own reference disk image to be mounted to the workflow task VMs

Currently, Terra allows users to mount a reference disk image when running a workflow, allowing a task to mount the disk with reference files instead of localizing it to the running VM.  Problem: T...

• Beri
• Edited July 27, 2021 20:59
• 3 followers
• 3 comments
• 4 votes

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

Hi Dan Spagnolo For compute resource error messages try increasing the notebook runtime. Follow along this article for details Understanding-and-Customizing-your-Notebook-Runtime. If you think the ...

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• June 03, 2020 11:49
• 0 votes