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 cf815a5178cb9ab03c769f5acc11de7fe5f8fd8e..d9023c92186ca6fda034cbf4552accdb5c069364 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@ -1,9 +1,9 @@
 cwlVersion: v1.1
 class: Workflow
-label: Variant calling workflow for given interval 
+label: Variant calling workflow for given interval
 
 requirements:
-  - class: SubworkflowFeatureRequirement
+  SubworkflowFeatureRequirement: {}
 
 inputs:
   bam:
@@ -24,10 +24,16 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: 
+  sample:
     type: string
     label: Sample Name
   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
@@ -35,7 +41,7 @@ inputs:
       - .tbi
   intervallist:
     type: File
-    label: Scatter intervals file 
+    label: Scatter intervals file
 
 outputs:
   gvcf:
@@ -52,11 +58,12 @@ steps:
       reference: reference
       sample: sample
       knownsites1: knownsites1
+      knownsites2: knownsites2
       intervallist: intervallist
     out: [recaltable]
   applyBQSR:
     run: gatk-applyBSQR-with-interval.cwl
-    in: 
+    in:
       reference: reference
       bam: bam
       sample: sample
@@ -73,7 +80,7 @@ steps:
     out: [gvcf]
   selectvariants:
     run: gatk-selectvariants.cwl
-    in: 
+    in:
       gvcf: haplotypecaller/gvcf
       reference: reference
       sample: sample
@@ -86,6 +93,6 @@ $namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/
 
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl