X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/4bb5fb748cbceab1f23d3972cd502e94711fc7c9..ec300c76b5a3f927c3cd5035669b70847ade3854:/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 58e38cb..8cbcf5e 100644
--- a/WGS-processing/cwl/wgs-processing-wf.cwl
+++ b/WGS-processing/cwl/wgs-processing-wf.cwl
@@ -22,6 +22,8 @@ inputs:
       - .sa
       - .fai
       - ^.dict
+  fullintervallist:
+    type: File
   knownsites:
     type: File
     format: edam:format_3016 # VCF
@@ -40,11 +42,11 @@ 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:
@@ -53,11 +55,10 @@ outputs:
     outputSource: bwamem-gatk-report/gvcf
     format: edam:format_3016 # GVCF
     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:
@@ -75,6 +76,7 @@ steps:
       fastq1: getfastq/fastq1
       fastq2: getfastq/fastq2
       reference: reference
+      fullintervallist: fullintervallist
       sample: getfastq/sample
       knownsites: knownsites
       scattercount: scattercount
@@ -91,6 +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