Problem creating gatk-sv Workflow in AWS HealthOmics

[eprdz]

Hello,

Is it possible to upload this workflow to AWS HealthOmics? I have worked with other GATK and WARP workflows smoothly, but I'm having problems creating a workflow with this one.

Everything seems to be OK but in the end, the creation always fails with a huge error text with a lot of warnings of the AWS linter. I don't know if it might be because of the size of the workflow, as other workflows with linter warnings have been correctly uploaded in HealthOmics.

I was wondering if you knew anything about it.

Thank you in advance.

[mwalker174]

Hi @eprdz thanks for your question, I'm afraid we don't support any backends except Google Cloud at the moment. We do validate our WDLs with miniwdl but perhaps not with the same stringency as the linter is configured on AWS.

[eprdz]

Thanks for your answer. I managed to successfully upload the GATK SV Single Sample Workflow to AWS HealthOmics.
Is there a significant difference between the GATK SV Single Sampleworkflow that I uploaded and the current workflow for single sample mode?
Thank you again in advance.

[mwalker174]

That version is deprecated, but it's possible that it's still runnable. A substantial number of improvements have been made since that was published.