- workflowmapper = super(RunnerJob, self).arvados_job_spec(dry_run=dry_run, pull_image=pull_image, **kwargs)
-
- # Need to filter this out, gets added by cwltool when providing
- # parameters on the command line, and arv-run-pipeline-instance doesn't
- # like it.
- if "job_order" in self.job_order:
- del self.job_order["job_order"]
+ if self.tool.tool["id"].startswith("keep:"):
+ self.job_order["cwl:tool"] = self.tool.tool["id"][5:]
+ else:
+ packed = packed_workflow(self.arvrunner, self.tool)
+ wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed)
+ self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh