Updating cwl and yml for intervals and other changes

[arvados-tutorial.git] / WGS-processing / cwl / helper / scatter-gatk-wf-with-interval.cwl

diff --git a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
index 75c605b822bf07b8fca8e3e66edc4e152153c014..80d7601115c8ef2cb1839e273266cdc1947ce4dd 100644 (file)
--- a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
@@ -3,8 +3,8 @@ class: Workflow
 label: Scattered variant calling workflow
 
 requirements:
-  - class: SubworkflowFeatureRequirement
-  - class: ScatterFeatureRequirement
+  SubworkflowFeatureRequirement: {}
+  ScatterFeatureRequirement: {}
 
 inputs:
   bam:
@@ -25,6 +25,9 @@ inputs:
       - .sa
       - .fai
       - ^.dict
+  fullintervallist:
+    type: File
+    label: Full list of intervals to operate over
   sample:
     type: string
     label: Sample Name
@@ -52,6 +55,7 @@ steps:
     run: gatk-splitintervals.cwl
     in:
       reference: reference
+      fullintervallist: fullintervallist
       sample: sample
       scattercount: scattercount
     out: [intervalfiles]