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theiagen / public_health_viral_genomics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
https://public-health-viral-genomics-theiagen.readthedocs.io/
GNU Affero General Public License v3.0
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ensure WDL compatibility with Azure #187

Closed vsmalladi closed 1 year ago

vsmalladi commented 2 years ago

See compatibility notes here: https://github.com/microsoft/CromwellOnAzure/blob/master/docs/change-existing-WDL-for-Azure.md/#How-to-modify-an-existing-WDL-file-to-run-on-Cromwell-on-Azure

Mostly focused on making sure some of the runtime block items are specified in compatible ways (ie, that memory and disk always have units attached) and that we add a maxRetries synonym for wherever we specify preemptible. We might already be compatible, it's just worth going through and double checking...

kapsakcj commented 2 years ago

Thanks for letting us know and for the information! This will be a necessary change as Terra on Azure becomes available.

vsmalladi commented 2 years ago

Will try to do a pr next week to get this started