[ARVADOS] created: 966acb6ce28cdb4b0d30bdcd238cbbce73deaa87

[Git user]

        at  966acb6ce28cdb4b0d30bdcd238cbbce73deaa87 (commit)


commit 966acb6ce28cdb4b0d30bdcd238cbbce73deaa87
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jun 28 10:03:30 2016 -0400

    9442: Override kwargs["outdir"] so that $(runtime.outdir) is set correctly.

diff --git a/sdk/cwl/arvados_cwl/arvtool.py b/sdk/cwl/arvados_cwl/arvtool.py
index ecc913e..7347eac 100644
--- a/sdk/cwl/arvados_cwl/arvtool.py
+++ b/sdk/cwl/arvados_cwl/arvtool.py
@@ -28,3 +28,7 @@ class ArvadosCommandTool(CommandLineTool):
                                  "$(task.keep)/%s",
                                  "$(task.keep)/%s/%s",
                                  **kwargs)
+
+    def job(self, joborder, output_callback, **kwargs):
+        kwargs["outdir"] = "$(task.outdir)"
+        return super(ArvadosCommandTool, self).job(joborder, output_callback, **kwargs)

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