diff --git a/cwltool/job.py b/cwltool/job.py
index 647803d2b..92c62d774 100644
--- a/cwltool/job.py
+++ b/cwltool/job.py
@@ -69,7 +69,7 @@
     if sp.stdin:
         sp.stdin.close()
     rcode = sp.wait()
-    if isinstance(stdin, file):
+    if stdin is not subprocess.PIPE:
         stdin.close()
     if stdout is not sys.stderr:
         stdout.close()