Switching variable knownsites1 to knownsites

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

diff --git a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
index 71cb27fa94283c45f2faae389735ad56f27421f8..6df9de12675d1a00af561adb2d874376c9cf4801 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
@@ -44,7 +44,7 @@ inputs:
   sample:
     type: string
     label: Sample Name
-  knownsites1: 
+  knownsites: 
     type: File
     format: edam:format_3016 # VCF
     label: VCF of known polymorphic sites for BQSR
@@ -57,7 +57,7 @@ inputs:
 outputs:
   recaltable:
     type: File
-    label: Recalibration table
+    label: Recalibration table for given interval
     outputBinding:
       glob: "*.table"
 
@@ -72,7 +72,7 @@ arguments:
   - prefix: "-I"
     valueFrom: $(inputs.bam.basename)
   - prefix: "--known-sites"
-    valueFrom: $(inputs.knownsites1)
+    valueFrom: $(inputs.knownsites)
   - prefix: "-L"
     valueFrom: $(inputs.intervallist)
   - prefix: "-O"
@@ -84,6 +84,8 @@ s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
 $namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/
+ arv: "http://arvados.org/cwl#"
+ cwltool: "http://commonwl.org/cwltool#"
 
 $schemas:
  - https://schema.org/version/latest/schema.rdf