No issue #

Arvados-DCO-1.1-Signed-off-by: Sarah Zaranek <swz@curii.com>

diff --git a/cwl/lightning/lightning-choose-samples.cwl b/cwl/lightning/lightning-choose-samples.cwl
index 92bef11336d1936794ed8318fd4acbb2376a1f3a..f03c585aba96ae6f953137eb5490eaae2e9b053d 100644 (file)
--- a/cwl/lightning/lightning-choose-samples.cwl
+++ b/cwl/lightning/lightning-choose-samples.cwl
@@ -44,7 +44,7 @@ arguments:
   - prefix: "-case-control-file="
     valueFrom: $(inputs.phenotypesdir)
     separate: false
-  - "-case-control-column=DISEASE"
+  - "-case-control-column=AD"
   - prefix: "-training-set-size="
     valueFrom: $(inputs.trainingsetsize)
     separate: false

diff --git a/cwl/lightning/lightning-import.cwl b/cwl/lightning/lightning-import.cwl
index d32a2d5fe1601a6f8d135c2178a60e763d1d8f0a..10aa3088091f6ffd30decaa28ee97607004c9f7d 100644 (file)
--- a/cwl/lightning/lightning-import.cwl
+++ b/cwl/lightning/lightning-import.cwl
@@ -9,6 +9,9 @@ class: CommandLineTool
 requirements:
   NetworkAccess:
     networkAccess: true
+  EnvVarRequirement: 
+    envDef:
+      GOMAXPROCS: "48"
 hints:
   DockerRequirement:
     dockerPull: lightning
@@ -41,7 +44,6 @@ arguments:
   - "-output-tiles=true"
   - "-batches=1"
   - "-batch=0"
-  - "-GOMAXPROCS=48"
   - prefix: "-save-incomplete-tiles="
     valueFrom: $(inputs.saveincomplete)
     separate: false