+ workflowcollection = workflowmapper.mapper(self.tool.tool["id"])[1]
+ if workflowcollection.startswith("keep:"):
+ workflowcollection = workflowcollection[5:workflowcollection.index('/')]
+ workflowname = os.path.basename(self.tool.tool["id"])
+ workflowpath = "/var/lib/cwl/workflow/%s" % workflowname
+ container_req["mounts"]["/var/lib/cwl/workflow"] = {
+ "kind": "collection",
+ "portable_data_hash": "%s" % workflowcollection
+ }
+ elif workflowcollection.startswith("arvwf:"):
+ workflowpath = "/var/lib/cwl/workflow.json#main"
+ fetcher = CollectionFetcher({}, None,
+ api_client=self.arvrunner.api,
+ keep_client=self.arvrunner.keep_client)
+ wfobj = yaml.safe_load(fetcher.fetch_text(workflowcollection))
+ container_req["mounts"]["/var/lib/cwl/workflow.json"] = {
+ "kind": "json",
+ "json": wfobj
+ }
+
+ command = ["arvados-cwl-runner", "--local", "--api=containers"]
+ if self.output_name:
+ command.append("--output-name=" + self.output_name)
+
+ if self.output_tags:
+ command.append("--output-tags=" + self.output_tags)
+
+ if self.enable_reuse:
+ command.append("--enable-reuse")
+ else:
+ command.append("--disable-reuse")
+
+ command.extend([workflowpath, jobpath])
+
+ container_req["command"] = command
+
+ return container_req
+
+