10081: Rename cwl.input.json to cwl.input.yml, fix test.

[arvados.git] / sdk / cwl / arvados_cwl / arvtool.py

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index 7347eacaacd3044367460b43b889f004600651fd..987ce8967aef2934d6d0f17bf3316e9eb85d70cf 100644 (file)
--- 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 +31,12 @@ 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"] = "$(task.outdir)"
+            kwargs["tmpdir"] = "$(task.tmpdir)"
+            kwargs["docker_tmpdir"] = "$(task.tmpdir)"
         return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)