Adding metatdata and labels
[arvados-tutorial.git] / WGS-processing / cwl / helper / report-wf.cwl
index 3403ebbe7dfb880d5a5d44b8c7a05c5c1c6a6d36..b53f385d85d690fbe4b7a5d241254f0add9618f4 100644 (file)
@@ -1,45 +1,68 @@
 cwlVersion: v1.1
 class: Workflow
+label: Report generation workflow
 
 inputs:
   gvcf: 
     type: File
-  samplename:
+    format: edam:format_3016 # GVCF
+    label: Gathered GVCF
+  sample:
     type: string
+    label: Sample Name
   clinvarvcf:
     type: File
+    format: edam:format_3016 # VCF
+    label: Reference VCF for ClinVar
   reportfunc:
     type: File
+    label: Function used to create HTML report
   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_1964 # HTML
+    label: ClinVar variant report
     outputSource: generate-report/report
 
 steps:
   gvcf-to-vcf:
-    run: ./helper/gvcf-to-vcf.cwl
+    run: gvcf-to-vcf.cwl
     in:
       gvcf: gvcf
-      samplename: samplename
+      sample: sample
     out: [vcf]
-
   annotate:
-    run: ./helper/annotate-vcf.cwl
+    run: annotate-vcf.cwl
     in:
       vcf: gvcf-to-vcf/vcf
       clinvarvcf: clinvarvcf
     out: [reporttxt]
-
   generate-report:
-    run: ./helper/generate-report.cwl
+    run: generate-report.cwl
     in:
       reportfunc: reportfunc
       sampletxt: annotate/reporttxt
+      sample: sample
       headhtml: headhtml
       tailhtml: tailhtml
     out: [report]
+
+s:codeRepository: https://github.com/arvados/arvados-tutorial
+s:license: https://www.gnu.org/licenses/agpl-3.0.en.html
+
+$namespaces:
+ s: https://schema.org/
+ edam: http://edamontology.org/
+
+$schemas:
+ - https://schema.org/version/latest/schema.rdf
+ - http://edamontology.org/EDAM_1.18.owl