X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/92172b0bceb7af669a8dd09cea04c93e041dfe2e..f80667171aa3d9efb35d60faa4d9cdabb50ca330:/WGS-processing/cwl/helper/report-wf.cwl?ds=sidebyside

diff --git a/WGS-processing/cwl/helper/report-wf.cwl b/WGS-processing/cwl/helper/report-wf.cwl
index 3403ebb..9e675ff 100644
--- 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