From 639b5ed3a0530cedcf4bc6f9771c99249a5981cc Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 8 Aug 2018 16:47:52 +0200
Subject: [PATCH] add SortVcf task
---
picard.wdl | 35 +++++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)
diff --git a/picard.wdl b/picard.wdl
index ac372b1..4132754 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -378,3 +378,38 @@ task ScatterIntervalList {
memory: ceil(memory * memoryMultiplier)
}
}
+
+task SortVcf {
+ input {
+ String? preCommand
+ String? picardJar
+
+ Array[File]+ vcfFiles
+ String outputVcf
+
+ Int memory = 4
+ Float memoryMultiplier = 3.0
+ }
+
+ String toolCommand = if defined(picardJar)
+ then "java -Xmx" + memory + "G -jar " + picardJar
+ else "picard -Xmx" + memory + "G"
+
+ command {
+ set -e -o pipefail
+ ~{preCommand}
+ ~{toolCommand} \
+ SortVcf \
+ I=~{sep=" I=" vcfFiles} \
+ O=outputVcf
+ }
+
+ output {
+ File vcfFile = outputVcf
+ File vcfIndex = outputVcf + ".tbi"
+ }
+
+ runtime {
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
\ No newline at end of file
--
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