From fad48898579fd48cef71bc46cb56f66d6e3fb07f Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Thu, 5 Mar 2020 13:44:51 +0000
Subject: [PATCH] Adding cwl to annotate and generate report
 Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com> no issue #

---
 cwl/annotate-vcf.cwl    | 37 +++++++++++++++++++++++++++++++++++++
 cwl/generate-report.cwl | 36 ++++++++++++++++++++++++++++++++++++
 2 files changed, 73 insertions(+)
 create mode 100644 cwl/annotate-vcf.cwl
 create mode 100644 cwl/generate-report.cwl

diff --git a/cwl/annotate-vcf.cwl b/cwl/annotate-vcf.cwl
new file mode 100644
index 0000000..5a5c84f
--- /dev/null
+++ b/cwl/annotate-vcf.cwl
@@ -0,0 +1,37 @@
+cwlVersion: v1.1
+class: CommandLineTool
+
+requirements:
+  - class: DockerRequirement
+    dockerPull: curii/clinvar-report
+  - class: ShellCommandRequirement
+
+hints:
+  ResourceRequirement:
+    ramMin: 10000
+    coresMin: 4
+
+stdout: $(inputs.vcf.nameroot).txt
+
+arguments:
+  - bcftools
+  - annotate
+  - prefix: "-a"
+    valueFrom: $(inputs.clinvarvcf.path)
+  - prefix: "-c"
+    valueFrom: "ID,INFO"
+  - $(inputs.vcf.path)
+  - {valueFrom: '|', shellQuote: false}
+  - bcftools
+  - filter
+  - prefix: "-i"
+    valueFrom: "INFO/ALLELEID>=1"
+
+inputs: 
+  vcf:
+    type: File
+  clinvarvcf:
+    type: File
+  
+outputs:
+  report: stdout
diff --git a/cwl/generate-report.cwl b/cwl/generate-report.cwl
new file mode 100644
index 0000000..0c438d4
--- /dev/null
+++ b/cwl/generate-report.cwl
@@ -0,0 +1,36 @@
+cwlVersion: v1.1
+class: CommandLineTool
+
+requirements:
+  DockerRequirement:
+    dockerPull: curii/clinvar-report
+
+hints:
+  ResourceRequirement:
+    ramMin: 10000
+    coresMin: 4    
+
+baseCommand: python
+
+arguments:
+  - $(inputs.reportfunc)
+  - $(inputs.sampletxt)
+  - $(inputs.sampletxt.basename)
+  - $(inputs.headhtml)
+  - $(inputs.tailhtml)
+
+inputs:
+  reportfunc:
+    type: File
+  sampletxt:
+    type: File
+  headhtml:
+    type: File
+  tailhtml:
+    type: File
+    
+outputs:
+  report:
+    type: File
+    outputBinding:
+      glob: "*html"
-- 
2.30.2