Updating to allow for two vcfs of known sites

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

diff --git a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
index a5d1993652859aacc0430f982f2b50851336d8ac..d9023c92186ca6fda034cbf4552accdb5c069364 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@ -3,7 +3,7 @@ class: Workflow
 label: Variant calling workflow for given interval
 
 requirements:
-  - class: SubworkflowFeatureRequirement
+  SubworkflowFeatureRequirement: {}
 
 inputs:
   bam:
@@ -27,7 +27,13 @@ inputs:
   sample:
     type: string
     label: Sample Name
-  knownsites:
+  knownsites1:
+    type: File
+    format: edam:format_3016 # VCF
+    label: VCF of known polymorphic sites for BQSR
+    secondaryFiles:
+      - .idx
+  knownsites2:
     type: File
     format: edam:format_3016 # VCF
     label: VCF of known polymorphic sites for BQSR
@@ -51,7 +57,8 @@ steps:
       bam: bam
       reference: reference
       sample: sample
-      knownsites: knownsites
+      knownsites1: knownsites1
+      knownsites2: knownsites2
       intervallist: intervallist
     out: [recaltable]
   applyBQSR: