Test latest version of Cromwell - Githubissues

wustl-oncology / cloud-workflows

Infrastructure and tooling required to get genomic workflows running in the cloud

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Test latest version of Cromwell #38

Open malachig opened 9 months ago

malachig commented 9 months ago

Upcoming changes to the Google Life Sciences API that Cromwell currently uses have been announced: sunsetting this service and requiring migration to GCP Batch instead.

In theory, updates to Cromwell to allow use of the Batch service will make this change mostly seamless to us. However we need to test this and make updates to how our configuration files are created.

First we should test simply updating Cromwell to the latest version without changing anything else.
Assuming (1) works, test Cromwell with an updated Cromwell config that specifies use of Batch

Documentation on Google Batch and Cromwell:

https://cromwell.readthedocs.io/en/develop/tutorials/Batch101/
https://cromwell.readthedocs.io/en/develop/backends/GCPBatch/
https://cloud.google.com/batch/docs/migrate-to-batch-from-cloud-life-sciences (see Cromwell section) The current config gets generated by : https://github.com/wustl-oncology/cloud-workflows/blob/1e55fbd4acb4bf5647b466fe802529c0cd360724/manual-workflows/resources.sh#L125-L143