Updating to allow for two vcfs of known sites

[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 7e5bf4df4bc863807a4136547ab794af374cb69e..2de30a62b88d0a0923b6951eaa05b9cf31c0ddc2 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl
@@ -1,13 +1,10 @@
 cwlVersion: v1.1
 class: CommandLineTool
-label: Generate recalibration table for BQSR 
+label: Generate recalibration table for BQSR
 
 requirements:
   DockerRequirement:
     dockerPull: broadinstitute/gatk:4.1.7.0
-  InitialWorkDirRequirement:
-    listing:
-      - $(inputs.bam)
 
 hints:
   arv:RuntimeConstraints:
@@ -44,7 +41,13 @@ inputs:
   sample:
     type: string
     label: Sample Name
-  knownsites1: 
+  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
@@ -70,9 +73,11 @@ arguments:
   - prefix: "-R"
     valueFrom: $(inputs.reference)
   - prefix: "-I"
-    valueFrom: $(inputs.bam.basename)
+    valueFrom: $(inputs.bam)
   - prefix: "--known-sites"
     valueFrom: $(inputs.knownsites1)
+  - prefix: "--known-sites"
+    valueFrom: $(inputs.knownsites2)
   - prefix: "-L"
     valueFrom: $(inputs.intervallist)
   - prefix: "-O"
@@ -87,6 +92,6 @@ $namespaces:
  arv: "http://arvados.org/cwl#"
  cwltool: "http://commonwl.org/cwltool#"
 
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl