[ARVADOS] updated: 1.1.4-251-g25cdd13
Git user
git at public.curoverse.com
Thu May 10 11:03:45 EDT 2018
Summary of changes:
sdk/cwl/arvados_cwl/arvworkflow.py | 5 +++++
1 file changed, 5 insertions(+)
via 25cdd138fccebc90086e0106e8b71273a990acf4 (commit)
from 71c1fb04107bb3d9411dd9f016cd0bf1b40f0e86 (commit)
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commit 25cdd138fccebc90086e0106e8b71273a990acf4
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date: Thu May 10 11:03:29 2018 -0400
12256: Comments about workflow references / extra files.
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>
diff --git a/sdk/cwl/arvados_cwl/arvworkflow.py b/sdk/cwl/arvados_cwl/arvworkflow.py
index 05d4648..6f731fd 100644
--- a/sdk/cwl/arvados_cwl/arvworkflow.py
+++ b/sdk/cwl/arvados_cwl/arvworkflow.py
@@ -182,6 +182,8 @@ class ArvadosWorkflow(Workflow):
uri,
False)
+ # Discover files/directories referenced by the
+ # workflow (mainly "default" values)
visit_class(packed, ("File", "Directory"), self.wf_reffiles.append)
@@ -216,6 +218,9 @@ class ArvadosWorkflow(Workflow):
"/keep/%s/%s",
**kwargs)
+ # For containers API, we need to make sure any extra
+ # referenced files (ie referenced by the workflow but
+ # not in the inputs) are included in the mounts.
kwargs["extra_reffiles"] = copy.deepcopy(self.wf_reffiles)
def keepmount(obj):
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