diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py
index 8949d36be3..becc6b4364 100644
--- a/nipype/pipeline/plugins/base.py
+++ b/nipype/pipeline/plugins/base.py
@@ -543,7 +543,9 @@ def _submit_job(self, node, updatehash=False):
         pyscript = create_pyscript(node, updatehash=updatehash)
         batch_dir, name = os.path.split(pyscript)
         name = ".".join(name.split(".")[:-1])
-        batchscript = "\n".join((self._template, "%s %s" % (sys.executable, pyscript)))
+        batchscript = "\n".join(
+            (self._template.rstrip("\n"), "%s %s" % (sys.executable, pyscript))
+        )
         batchscriptfile = os.path.join(batch_dir, "batchscript_%s.sh" % name)
         with open(batchscriptfile, "wt") as fp:
             fp.writelines(batchscript)