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)
+ packed = packed_workflow(self.arvrunner, self.tool, self.merged_map)
wf_pdh = upload_workflow_collection(self.arvrunner, self.name, packed)
self.job_order["cwl:tool"] = "%s/workflow.cwl#main" % wf_pdh
if self.on_error:
self.job_order["arv:on_error"] = self.on_error
+ if kwargs.get("debug"):
+ self.job_order["arv:debug"] = True
+
return {
"script": "cwl-runner",
"script_version": "master",
}
def __init__(self, runner, tool, job_order, enable_reuse, uuid,
- submit_runner_ram=0, name=None):
+ submit_runner_ram=0, name=None, merged_map=None):
self.runner = runner
self.tool = tool
self.job = RunnerJob(
output_name=None,
output_tags=None,
submit_runner_ram=submit_runner_ram,
- name=name)
+ name=name,
+ merged_map=merged_map)
self.uuid = uuid
def pipeline_component_spec(self):