Updating cwl and yml for intervals and other changes

[arvados-tutorial.git] / 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 a6218bdaa79bd28f83a2cd91087fca673999cf8a..8cbcf5ee03b17f7d5800b611fd29a4d69cfcc105 100644 (file)
--- a/WGS-processing/cwl/wgs-processing-wf.cwl
+++ b/WGS-processing/cwl/wgs-processing-wf.cwl
@@ -22,9 +22,8 @@ inputs:
       - .sa
       - .fai
       - ^.dict
-  sample: 
-    type: string
-    label: Sample name
+  fullintervallist:
+    type: File
   knownsites:
     type: File
     format: edam:format_3016 # VCF
@@ -43,11 +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:
@@ -55,12 +54,11 @@ 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:
@@ -78,6 +76,7 @@ steps:
       fastq1: getfastq/fastq1
       fastq2: getfastq/fastq2
       reference: reference
+      fullintervallist: fullintervallist
       sample: getfastq/sample
       knownsites: knownsites
       scattercount: scattercount
@@ -94,6 +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