Updating HTML edam comments

[arvados-tutorial.git] / WGS-processing / cwl / helper / report-wf.cwl

diff --git a/WGS-processing/cwl/helper/report-wf.cwl b/WGS-processing/cwl/helper/report-wf.cwl
index 0029018394d7aa1c2dd170860196efef9ed39a3a..9e675ff81e6408446c66bdc056040d3169b39d25 100644 (file)
--- a/WGS-processing/cwl/helper/report-wf.cwl
+++ b/WGS-processing/cwl/helper/report-wf.cwl
@@ -3,11 +3,11 @@ class: Workflow
 label: Report generation workflow
 
 inputs:
-  gvcf: 
+  gvcf:
     type: File
     format: edam:format_3016 # GVCF
     label: Gathered GVCF
-  samplename:
+  sample:
     type: string
     label: Sample Name
   clinvarvcf:
@@ -19,9 +19,9 @@ inputs:
     label: Function used to create HTML report
   headhtml:
     type: File
-    format: edam:format_2331# HTML
+    format: edam:format_2331 # HTML
     label: Header for HTML report
-  tailhtml:   
+  tailhtml:
     type: File
     format: edam:format_2331 # HTML
     label: Footer for HTML report
@@ -29,7 +29,7 @@ inputs:
 outputs:
   report:
     type: File
-    format: edam:format_1964 # HTML
+    format: edam:format_2331 # HTML
     label: ClinVar variant report
     outputSource: generate-report/report
 
@@ -38,21 +38,20 @@ steps:
     run: gvcf-to-vcf.cwl
     in:
       gvcf: gvcf
-      samplename: samplename
+      sample: sample
     out: [vcf]
-
   annotate:
     run: annotate-vcf.cwl
     in:
       vcf: gvcf-to-vcf/vcf
       clinvarvcf: clinvarvcf
     out: [reporttxt]
-
   generate-report:
     run: generate-report.cwl
     in:
       reportfunc: reportfunc
       sampletxt: annotate/reporttxt
+      sample: sample
       headhtml: headhtml
       tailhtml: tailhtml
     out: [report]
@@ -64,6 +63,6 @@ $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