Updating to allow for two vcfs of known sites

[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 9752edb90f3efb83f3221ca22c9a33b402a050e7..13bd4af04c3528e384078e073c4e722823e498ec 100644 (file)
--- a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl
@@ -25,10 +25,19 @@ inputs:
       - .sa
       - .fai
       - ^.dict
+  fullintervallist:
+    type: File
+    label: Full list of intervals to operate over
   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
@@ -52,6 +61,7 @@ steps:
     run: gatk-splitintervals.cwl
     in:
       reference: reference
+      fullintervallist: fullintervallist
       sample: sample
       scattercount: scattercount
     out: [intervalfiles]
@@ -63,7 +73,8 @@ steps:
       bam: bam
       reference: reference
       sample: sample
-      knownsites: knownsites
+      knownsites1: knownsites1
+      knownsites2: knownsites2
       intervallist: splitintervals/intervalfiles
     out: [gvcf]