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 98758d1e9e5474c4cb8e2cd7dd6aed3c9af12ee3..4909bc7412d0ebfcf64d12f652604d6a556a8da9 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-splitintervals.cwl
+++ b/WGS-processing/cwl/helper/gatk-splitintervals.cwl
@@ -32,6 +32,9 @@ inputs:
       - .sa
       - .fai
       - ^.dict
+  fullintervallist:
+    type: File
+    label: Full list of intervals to operate over
   sample:
     type: string
     label: Sample Name
@@ -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"