"kind": "collection",
"portable_data_hash": "%s" % workflowcollection
}
+ elif self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
+ workflowpath = "/var/lib/cwl/workflow.json#main"
+ record = self.arvrunner.api.workflows().get(uuid=self.embedded_tool.tool["id"][6:33]).execute(num_retries=self.arvrunner.num_retries)
+ packed = yaml.safe_load(record["definition"])
+ container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
+ "kind": "json",
+ "content": packed
+ }
+ container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
else:
packed = packed_workflow(self.arvrunner, self.embedded_tool, self.merged_map, runtimeContext, git_info)
workflowpath = "/var/lib/cwl/workflow.json#main"
"kind": "json",
"content": packed
}
- if self.embedded_tool.tool.get("id", "").startswith("arvwf:"):
- container_req["properties"]["template_uuid"] = self.embedded_tool.tool["id"][6:33]
container_req["properties"].update({k.replace("http://arvados.org/cwl#", "arv:"): v for k, v in git_info.items()})