From 9a082726b10c00676607ff76346be674dbb15a7f Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Mon, 29 Oct 2018 15:26:26 +0100
Subject: [PATCH] add GatherVcfs
---
picard.wdl | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/picard.wdl b/picard.wdl
index 6a52ee4..4b70a0b 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -240,6 +240,40 @@ task GatherBamFiles {
}
}
+task GatherVcfs {
+ input {
+ String? preCommand
+ Array[File]+ inputVcfs
+ Array[File]+ inputVcfIndexes
+ String outputVcfPath
+ String? picardJar
+
+ 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} \
+ GatherVcfs \
+ INPUT=~{sep=' INPUT=' inputVcfs} \
+ OUTPUT=~{outputVcfPath}
+ }
+
+ output {
+ File outputVcf = outputVcfPath
+ }
+
+ runtime {
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
# Mark duplicate reads to avoid counting non-independent observations
task MarkDuplicates {
input {
--
GitLab