Rearranging for clarity

[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
new file mode 100644 (file)
index 0000000..de8ab3f
--- /dev/null
+++ b/WGS-processing/cwl/helper/report-wf.cwl
@@ -0,0 +1,45 @@
+cwlVersion: v1.1
+class: Workflow
+
+inputs:
+  gvcf: 
+    type: File
+  samplename:
+    type: string
+  clinvarvcf:
+    type: File
+  reportfunc:
+    type: File
+  headhtml:
+    type: File
+  tailhtml:   
+    type: File
+
+outputs:
+  report:
+    type: File
+    outputSource: generate-report/report
+
+steps:
+  gvcf-to-vcf:
+    run: gvcf-to-vcf.cwl
+    in:
+      gvcf: gvcf
+      samplename: samplename
+    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
+      headhtml: headhtml
+      tailhtml: tailhtml
+    out: [report]