Updating cwl and yml for intervals and other changes

[arvados-tutorial.git] / WGS-processing / cwl / helper / gatk-splitintervals.cwl

diff --git a/WGS-processing/cwl/helper/gatk-splitintervals.cwl b/WGS-processing/cwl/helper/gatk-splitintervals.cwl
index 9e2644797a107dbc70d942ba25698e8f3072e6ce..4909bc7412d0ebfcf64d12f652604d6a556a8da9 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-splitintervals.cwl
+++ b/WGS-processing/cwl/helper/gatk-splitintervals.cwl
@@ -32,10 +32,13 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: 
+  fullintervallist:
+    type: File
+    label: Full list of intervals to operate over
+  sample:
     type: string
     label: Sample Name
-  scattercount: 
+  scattercount:
     type: string
     label: Desired split for variant calling
 
@@ -54,6 +57,8 @@ arguments:
   - SplitIntervals
   - prefix: "-R"
     valueFrom: $(inputs.reference)
+  - prefix: "-L"
+    valueFrom: $(inputs.fullintervallist)
   - prefix: "--scatter-count"
     valueFrom: $(inputs.scattercount)
   - prefix: "--subdivision-mode"
@@ -70,6 +75,6 @@ $namespaces:
  arv: "http://arvados.org/cwl#"
  cwltool: "http://commonwl.org/cwltool#"
 
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl