add SV task: survivor.wdl

survivor.wdl

+version 1.0
+
+import "common.wdl"
+
+task Merge {
+    input{
+        Array[File] filePaths
+        Int breakpointDistance = 1000
+        Int suppVecs = 2
+        Int svType = 1
+        Int strandType = 1
+        Int distanceBySvSize = 0
+        Int minSize = 30
+        String sample
+        String outputPath
+        Int memory = 128
+    }
+
+    command <<< 
+        set -e
+        mkdir -p $(dirname ~{outputPath}) 
+        echo '~{sep="\n" filePaths}' > fileList
+        SURVIVOR merge \
+        fileList \
+        ~{breakpointDistance} \
+        ~{suppVecs} \
+        ~{svType} \
+        ~{strandType} \
+        ~{distanceBySvSize} \
+        ~{minSize} \
+        ~{outputPath}
+    >>> 
+
+    output {
+        File mergedVcf = "~{outputPath}"
+    }
+    
+    runtime {
+        docker: "quay.io/biocontainers/survivor:1.0.6--h6bb024c_0"
+        memory: memory
+    }
+}