Merge branch '12061-flaky-tests'
[arvados.git] / sdk / cwl / arvados_cwl / arvtool.py
index ddc270d7375a6719e2117766d954df294e50e7e9..fea6adfacc323539d7c2cd595f66d441859893b8 100644 (file)
@@ -24,7 +24,7 @@ class ArvadosCommandTool(CommandLineTool):
     def makePathMapper(self, reffiles, stagedir, **kwargs):
         # type: (List[Any], unicode, **Any) -> PathMapper
         if self.work_api == "containers":
-            return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
+            return ArvPathMapper(self.arvrunner, reffiles+kwargs.get("extra_reffiles", []), kwargs["basedir"],
                                  "/keep/%s",
                                  "/keep/%s/%s",
                                  **kwargs)
@@ -39,6 +39,7 @@ class ArvadosCommandTool(CommandLineTool):
         # Workaround for #13365
         builderargs = kwargs.copy()
         builderargs["toplevel"] = True
+        builderargs["tmp_outdir_prefix"] = ""
         builder = self._init_job(joborder, **builderargs)
         joborder = builder.job