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Updating yml for formats
[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 ee8ae4fdce5682340403ba4070a10fc52e1cb1f6..ea5b93b53224b3cdf7b79dfab25c8d8a7351657c 100644 (file)
--- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
+++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl
@@ -3,7 +3,7 @@ class: Workflow
 label: WGS processing workflow for single sample
 
 requirements:
 label: WGS processing workflow for single sample
 
 requirements:
-  - class: SubworkflowFeatureRequirement
+  SubworkflowFeatureRequirement: {}
 
 inputs:
   fastq1:
 
 inputs:
   fastq1:
@@ -119,7 +119,7 @@ steps:
     run: report-wf.cwl
     in:
       gvcf: haplotypecaller/gatheredgvcf
     run: report-wf.cwl
     in:
       gvcf: haplotypecaller/gatheredgvcf
-      samplename: sample
+      sample: sample
       clinvarvcf: clinvarvcf
       reportfunc: reportfunc
       headhtml: headhtml
       clinvarvcf: clinvarvcf
       reportfunc: reportfunc
       headhtml: headhtml
@@ -133,6 +133,6 @@ $namespaces:
  s: https://schema.org/
  edam: http://edamontology.org/
 
  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