[ARVADOS] created: 966acb6ce28cdb4b0d30bdcd238cbbce73deaa87
Git user
git at public.curoverse.com
Tue Jun 28 10:03:38 EDT 2016
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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