Bugfix .bai secondary file for ApplyBSQR behavior

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

diff --git a/WGS-processing/cwl/helper/generate-report.cwl b/WGS-processing/cwl/helper/generate-report.cwl
index 8ece243530d8cbd6f0ebb02c849783c0c6ba7b60..3773f7d7aa2289ad940ba3fc99a56762043e8e28 100644 (file)
--- a/WGS-processing/cwl/helper/generate-report.cwl
+++ b/WGS-processing/cwl/helper/generate-report.cwl
@@ -1,5 +1,6 @@
 cwlVersion: v1.1
 class: CommandLineTool
+label: Generate ClinVar Report
 
 requirements:
   DockerRequirement:
@@ -8,21 +9,32 @@ requirements:
 hints:
   ResourceRequirement:
     ramMin: 10000
-    coresMin: 4    
+    coresMin: 4
 
 inputs:
   reportfunc:
     type: File
+    label: Function used to create HTML report
   sampletxt:
     type: File
+    label: Annotated text from VCF
+  sample:
+    type: string
+    label: Sample Name
   headhtml:
     type: File
+    format: edam:format_2331 # HTML
+    label: Header for HTML report
   tailhtml:
     type: File
+    format: edam:format_2331 # HTML
+    label: Footer for HTML report
 
 outputs:
   report:
     type: File
+    format: edam:format_2331 # HTML
+    label: ClinVar variant report
     outputBinding:
       glob: "*html"
 
@@ -31,6 +43,14 @@ baseCommand: python
 arguments:
   - $(inputs.reportfunc)
   - $(inputs.sampletxt)
-  - $(inputs.sampletxt.basename)
+  - $(inputs.sample)
   - $(inputs.headhtml)
   - $(inputs.tailhtml)
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl