X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/966acb6ce28cdb4b0d30bdcd238cbbce73deaa87..d89fc97f4a7ee74edcb1a5856fec560c748b9086:/sdk/cwl/arvados_cwl/arvtool.py

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index 7347eacaac..7107ba0a30 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",
@@ -30,5 +31,10 @@ class ArvadosCommandTool(CommandLineTool):
                                  **kwargs)
 
     def job(self, joborder, output_callback, **kwargs):
-        kwargs["outdir"] = "$(task.outdir)"
+        if self.work_api == "containers":
+            kwargs["outdir"] = "/var/spool/cwl"
+            kwargs["docker_outdir"] = "/var/spool/cwl"
+        elif self.work_api == "jobs":
+            kwargs["outdir"] = "$(task.outdir)"
+            kwargs["docker_outdir"] = "$(task.outdir)"
         return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)