X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5acd68562b23c0293140a9de6443855b6612266b..6980748d61d4dff0ab95be4c65f55be47d13bb57:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 5e42df6241..19a6dd98b3 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -334,7 +334,8 @@ def upload_dependencies(arvrunner, name, document_loader,
                                  builder_job_order,
                                  discovered)
 
-    visit_class(workflowobj, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
+    copied, _ = document_loader.resolve_all(copy.deepcopy(cmap(workflowobj)), base_url=uri, checklinks=False)
+    visit_class(copied, ("CommandLineTool", "Workflow"), discover_default_secondary_files)
 
     for d in list(discovered):
         # Only interested in discovered secondaryFiles which are local