add SV task: delly.wdl

delly.wdl

+version 1.0
+
+import "common.wdl"
+
+task CallSV {
+    input {
+        IndexedBamFile bamFile
+        Reference reference
+        String outputPath        
+    }
+    
+
+    command <<<
+        set -e
+        mkdir -p $(dirname ~{outputPath})
+        delly call \
+        -o ~{outputPath} \
+        -g ~{reference.fasta} \
+        ~{bamFile.file}
+    >>>
+
+    output {
+        File dellyBcf = "~{outputPath}" 
+    }
+    
+    runtime {
+        docker: "quay.io/biocontainers/delly:0.8.1--h4037b6b_1"
+    }
+
+}