Test latest version of Cromwell

[malachig]

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.

1. First we should test simply updating Cromwell to the latest version without changing anything else.
2. 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 :
  

  cloud-workflows/manual-workflows/resources.sh

  Lines 125 to 143 in 1e55fbd

  	function generate_config {
  	cp $SRC_DIR/base_cromwell.conf $CONFIG_DIR/cromwell.conf
  	cat << EOF >> $CONFIG_DIR/cromwell.conf
  	backend.providers.default.config {
  	project = "$PROJECT"
  	root = "gs://$BUCKET/cromwell-executions"
  	genomics.compute-service-account = "$COMPUTE_ACCOUNT"
  	filesystems.gcs.project = "$PROJECT"
  	}
  	EOF
  	cat <<EOF > $CONFIG_DIR/workflow_options.json
  	{
  	"default_runtime_attributes": {
  	"preemptible": 1,
  	"maxRetries": 2
  	},
  	"final_workflow_log_dir": "gs://$BUCKET/final-logs",
  	"final_call_logs": "gs://$BUCKET/call-logs"
  	}