X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a9f1adf0a3e2df296ce0a8c0a1d735b7e5044baa..defaa234ca09f1c0a202a77d7660b75d3c12de02:/sdk/cwl/arvados_cwl/arvtool.py

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index a2dffa675a..987ce8967a 100644
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -17,7 +17,8 @@ class ArvadosCommandTool(CommandLineTool):
         elif self.work_api == "jobs":
             return ArvadosJob(self.arvrunner)
 
-    def makePathMapper(self, reffiles, **kwargs):
+    def makePathMapper(self, reffiles, stagedir, **kwargs):
+        # type: (List[Any], unicode, **Any) -> PathMapper
         if self.work_api == "containers":
             return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
                                  "/keep/%s",
@@ -32,6 +33,10 @@ class ArvadosCommandTool(CommandLineTool):
     def job(self, joborder, output_callback, **kwargs):
         if self.work_api == "containers":
             kwargs["outdir"] = "/var/spool/cwl"
+            kwargs["docker_outdir"] = "/var/spool/cwl"
         elif self.work_api == "jobs":
             kwargs["outdir"] = "$(task.outdir)"
+            kwargs["docker_outdir"] = "$(task.outdir)"
+            kwargs["tmpdir"] = "$(task.tmpdir)"
+            kwargs["docker_tmpdir"] = "$(task.tmpdir)"
         return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)