From 8479f908856abfc3d3ecc7c316c1e87767afe8e8 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 20 Feb 2019 13:41:45 +0100
Subject: [PATCH] fix gatk images
---
gatk.wdl | 25 ++++++++++++-------------
1 file changed, 12 insertions(+), 13 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 6e56e3d..edae6bf 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -15,7 +15,7 @@ task ApplyBQSR {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "3.8--5"
+ String dockerTag = "4.1.0.0--0"
}
String toolCommand = if defined(gatkJar)
@@ -68,7 +68,7 @@ task BaseRecalibrator {
Reference reference
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "3.8--5"
+ String dockerTag = "4.1.0.0--0"
}
Array[File]+ knownIndelsSitesVCFsArg = flatten([
@@ -118,7 +118,7 @@ task CombineGVCFs {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "3.8--5"
+ String dockerTag = "4.1.0.0--0"
}
String toolCommand = if defined(gatkJar)
@@ -159,7 +159,7 @@ task GatherBqsrReports {
Int memory = 4
Float memoryMultiplier = 3.0
- String dockerTag = "3.8--5"
+ String dockerTag = "4.1.0.0--0"
}
String toolCommand = if defined(gatkJar)
@@ -202,7 +202,7 @@ task GenotypeGVCFs {
Int memory = 6
Float memoryMultiplier = 2.0
- String dockerTag = "3.8--5"
+ String dockerTag = "4.1.0.0--0"
}
File dbsnpFile = if (defined(dbsnpVCF)) then select_first([dbsnpVCF]).file else ""
@@ -255,7 +255,7 @@ task HaplotypeCallerGvcf {
Int memory = 4
Float memoryMultiplier = 3
- String dockerTag = "3.8--5"
+ String dockerTag = "4.1.0.0--0"
}
File dbsnpFile = if (defined(dbsnpVCF)) then select_first([dbsnpVCF]).file else ""
@@ -267,8 +267,7 @@ task HaplotypeCallerGvcf {
command {
set -e -o pipefail
~{preCommand}
- ~{toolCommand} \
- HaplotypeCaller \
+ gatk --java-options -Xmx~{memory}G HaplotypeCaller \
-R ~{reference.fasta} \
-O ~{gvcfPath} \
-I ~{sep=" -I " inputBams} \
@@ -286,7 +285,7 @@ task HaplotypeCallerGvcf {
}
runtime {
- docker: "quay.io/biocontainers/gatk:" + dockerTag
+ docker: "quay.io/biocontainers/gatk4:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
@@ -306,7 +305,7 @@ task MuTect2 {
String? gatkJar
Int memory = 4
Float memoryMultiplier = 3
- String dockerTag = "3.8--5"
+ String dockerTag = "4.1.0.0--0"
}
String toolCommand = if defined(gatkJar)
@@ -334,7 +333,7 @@ task MuTect2 {
}
runtime {
- docker: "quay.io/biocontainers/gatk:" + dockerTag
+ docker: "quay.io/biocontainers/gatk4:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
@@ -351,7 +350,7 @@ task SplitNCigarReads {
Int memory = 4
Float memoryMultiplier = 4
- String dockerTag = "3.8--5"
+ String dockerTag = "4.1.0.0--0"
}
String toolCommand = if defined(gatkJar)
@@ -377,7 +376,7 @@ task SplitNCigarReads {
}
runtime {
- docker: "quay.io/biocontainers/gatk:" + dockerTag
+ docker: "quay.io/biocontainers/gatk4:" + dockerTag
memory: ceil(memory * memoryMultiplier)
}
}
--
GitLab