From 61c37d6e244d0b3f60adde666055ce4fd26b4dc7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ant=C3=B3nio=20Paulo?= <antonio.do.paulo@ist.utl.pt>
Date: Wed, 31 Jul 2019 18:57:56 +0200
Subject: [PATCH] add GATK MergeStats as a task
---
gatk.wdl | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
diff --git a/gatk.wdl b/gatk.wdl
index bf3d831..38c3485 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -264,6 +264,7 @@ task MuTect2 {
File? panelOfNormalsIndex
String? f1r2TarGz = "f1r2.tar.gz"
Array[File]+ intervals
+ String outputStats = outputVcf + ".stats"
Int memory = 4
Float memoryMultiplier = 3
@@ -290,6 +291,7 @@ task MuTect2 {
File vcfFile = outputVcf
File vcfFileIndex = outputVcf + ".tbi"
File f1r2File = f1r2TarGz
+ File stats = outputStats
}
runtime {
@@ -326,6 +328,33 @@ task LearnReadOrientationModel {
}
}
+task MergeStats {
+ input {
+ Array[File]+ stats
+
+ Int memory = 2
+ Float memoryMultiplier = 1.5
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ }
+
+ command {
+ set -e
+ gatk --java-options -Xmx~{memory}G \
+ MergeMutectStats \
+ -stats ~{sep=" -stats " stats} \
+ -O "merged.stats"
+ }
+
+ output {
+ File mergedStats = "merged.stats"
+ }
+
+ runtime {
+ docker: dockerImage
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
task SplitNCigarReads {
input {
File inputBam
--
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