From 334ee17c7ac79d66c0ab56aad1b84330ccdc772f Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Fri, 21 Jun 2019 11:25:44 +0200
Subject: [PATCH] add SV task: survivor.wdl
---
survivor.wdl | 42 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)
create mode 100644 survivor.wdl
diff --git a/survivor.wdl b/survivor.wdl
new file mode 100644
index 0000000..f4fdc4b
--- /dev/null
+++ b/survivor.wdl
@@ -0,0 +1,42 @@
+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
+ }
+}
--
GitLab