Updating to allow for two vcfs of known sites

[arvados-tutorial.git] / WGS-processing / cwl / helper / bwamem-gatk-report-wf.cwl

diff --git a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
index dbb1d5024731aa1923fa539217264e6a7070600c..76e4798bf270315a57d10a2363aa203487feedc1 100644 (file)
--- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@ -32,12 +32,18 @@ inputs:
   sample: 
     type: string
     label: Sample Name
   sample: 
     type: string
     label: Sample Name

-  knownsites:
+  knownsites1:

     type: File
     format: edam:format_3016 # VCF
     label: VCF of known polymorphic sites for BQSR
     secondaryFiles:
     type: File
     format: edam:format_3016 # VCF
     label: VCF of known polymorphic sites for BQSR
     secondaryFiles:

-      - .tbi   
+      - .idx 
+  knownsites2:
+    type: File
+    format: edam:format_3016 # VCF
+    label: VCF of known polymorphic sites for BQSR
+    secondaryFiles:
+      - .tbi  

   scattercount: 
     type: string
     label: Desired split for variant calling
   scattercount: 
     type: string
     label: Desired split for variant calling


@@ -117,7 +123,8 @@ steps:
       bam: samtools-index/indexedbam
       sample: sample
       scattercount: scattercount
       bam: samtools-index/indexedbam
       sample: sample
       scattercount: scattercount

-      knownsites: knownsites
+      knownsites1: knownsites1
+      knownsites2: knownsites2

     out: [gatheredgvcf]
   generate-report:
     run: report-wf.cwl
     out: [gatheredgvcf]
   generate-report:
     run: report-wf.cwl