From 8f237f88d58d9634814010e00ffe55e2cdde2334 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 28 Oct 2015 11:08:53 -0400 Subject: [PATCH] 7593: Generate files replaces $(task.keep)/ with keep: notation to reference keep files. --- sdk/cwl/arvados_cwl/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py index 1c118b9602..5000b97f01 100644 --- a/sdk/cwl/arvados_cwl/__init__.py +++ b/sdk/cwl/arvados_cwl/__init__.py @@ -107,7 +107,7 @@ class ArvadosJob(object): script_parameters["task.vwd"] = {} for t in self.generatefiles: if isinstance(self.generatefiles[t], dict): - src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"][13:]) + src, rest = self.arvrunner.fs_access.get_collection(self.generatefiles[t]["path"].replace("$(task.keep)/", "keep:")) vwd.copy(rest, t, source_collection=src) else: with vwd.open(t, "w") as f: -- 2.30.2