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 3403ebbe7dfb880d5a5d44b8c7a05c5c1c6a6d36..9e675ff81e6408446c66bdc056040d3169b39d25 100644 (file)
--- a/WGS-processing/cwl/helper/report-wf.cwl
+++ b/WGS-processing/cwl/helper/report-wf.cwl
@@ -1,45 +1,68 @@
 cwlVersion: v1.1
 class: Workflow
+label: Report generation workflow
 
 inputs:
-  gvcf: 
+  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
-  tailhtml:   
+    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
     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