X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/b8a53604de36eb2db95b492a5b5f74128a84aebf..d96d1f7cc83487a516eb2dd7ca12c47eec750235:/WGS-processing/cwl/wgs-processing-wf.cwl

diff --git a/WGS-processing/cwl/wgs-processing-wf.cwl b/WGS-processing/cwl/wgs-processing-wf.cwl
index a6218bd..a058969 100644
--- a/WGS-processing/cwl/wgs-processing-wf.cwl
+++ b/WGS-processing/cwl/wgs-processing-wf.cwl
@@ -22,9 +22,6 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: 
-    type: string
-    label: Sample name
   knownsites:
     type: File
     format: edam:format_3016 # VCF
@@ -43,11 +40,11 @@ inputs:
     label: Function used to create HTML report
   headhtml: 
     type: File
-    format: edam:format_1964 # HTML
+    format: edam:format_2331 # HTML
     label: Header for HTML report
   tailhtml: 
     type: File
-    format: edam:format_1964 # HTML
+    format: edam:format_2331 # HTML
     label: Footer for HTML report
 
 outputs:
@@ -55,12 +52,11 @@ outputs:
     type: File[]
     outputSource: bwamem-gatk-report/gvcf
     format: edam:format_3016 # GVCF
-    label: GVCFs generated from sets of fastqs
-    
+    label: GVCFs generated from GATK 
   report:
     type: File[]  
     outputSource: bwamem-gatk-report/report
-    format: edam:format_1964 # HTML
+    format: edam:format_2331 # HTML
     label: ClinVar variant reports 
 
 steps:
@@ -94,6 +90,6 @@ $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