15358: Add encoding option to CollectionFsAccess.open() and use in fetch_text()

[arvados.git] / sdk / cwl / arvados_cwl / arvworkflow.py

diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 3c60ac9fd58eebf3c9a8c87dcb8050f5132f9258..c6bcd04776920186d9973bdf662c1fe060b9b8c2 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -174,7 +174,8 @@ class ArvadosWorkflow(Workflow):
                 raise WorkflowException("%s object must have 'id'" % (self.tool["class"]))
         document_loader, workflowobj, uri = (self.doc_loader, self.doc_loader.fetch(self.tool["id"]), self.tool["id"])
 
-        discover_secondary_files(self.tool["inputs"], joborder)
+        discover_secondary_files(self.arvrunner.fs_access, builder,
+                                 self.tool["inputs"], joborder)
 
         with Perf(metrics, "subworkflow upload_deps"):
             upload_dependencies(self.arvrunner,