8653: Fix pathmapper API

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

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 50c51b0671a389a86e95c6cb3e64c1f14b0e5e99..0533b5e83a65dfda7cfe92f9a562ce70940bc0a6 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -575,8 +575,8 @@ class ArvadosCommandTool(CommandLineTool):
     def makeJobRunner(self):
         return ArvadosJob(self.arvrunner)
 
-    def makePathMapper(self, reffiles, input_basedir, **kwargs):
-        return ArvPathMapper(self.arvrunner, reffiles, input_basedir,
+    def makePathMapper(self, reffiles, **kwargs):
+        return ArvPathMapper(self.arvrunner, reffiles, kwargs["basedir"],
                              "$(task.keep)/%s",
                              "$(task.keep)/%s/%s",
                              **kwargs)