From a6f81d200e60e2c9e7cfb9449bfaf28fa8c5e002 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 17:16:22 +0200
Subject: [PATCH] add GATK LearnReadOrientationModel as a task
---
gatk.wdl | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
diff --git a/gatk.wdl b/gatk.wdl
index 578765b..bf3d831 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -298,6 +298,34 @@ task MuTect2 {
}
}
+task LearnReadOrientationModel {
+ input {
+ Array[File] f1r2TarGz
+
+ Int memory = 4
+ Float memoryMultiplier = 2
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ }
+
+ command {
+ set -e
+ gatk --java-options -Xmx~{memory}G \
+ LearnReadOrientationModel \
+ -I ~{sep=" -I " f1r2TarGz} \
+ -O "artifact-priors.tar.gz"
+ }
+
+ output {
+ File artifactPriorTable = "artifact-priors.tar.gz"
+ }
+
+
+ runtime {
+ docker: dockerImage
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
task SplitNCigarReads {
input {
File inputBam
--
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