From 959bf985ed283d374f747a4791bed1cde753c201 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 17 Jul 2020 11:09:48 +0200
Subject: [PATCH] Update default gatk image
---
gatk.wdl | 48 ++++++++++++++++++++++++------------------------
1 file changed, 24 insertions(+), 24 deletions(-)
diff --git a/gatk.wdl b/gatk.wdl
index 939513d..0f5218b 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -35,7 +35,7 @@ task AnnotateIntervals {
String memory = "3G"
String javaXmx = "2G"
Int timeMinutes = 5
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -96,7 +96,7 @@ task ApplyBQSR {
Int memoryMb = javaXmxMb + 512
Int javaXmxMb = 2048
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -168,7 +168,7 @@ task BaseRecalibrator {
Int memoryMb = javaXmxMb + 512
Int javaXmxMb = 1024
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -227,7 +227,7 @@ task CalculateContamination {
String memory = "13G"
String javaXmx = "12G"
Int timeMinutes = 180
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -271,7 +271,7 @@ task CallCopyRatioSegments {
String memory = "3G"
String javaXmx = "2G"
Int timeMinutes = 2
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -320,7 +320,7 @@ task CollectAllelicCounts {
String memory = "11G"
String javaXmx = "10G"
Int timeMinutes = 120
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -376,7 +376,7 @@ task CollectReadCounts {
String memory = "8G"
String javaXmx = "7G"
Int timeMinutes = 1 + ceil(size(inputBam, "G") * 5)
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -433,7 +433,7 @@ task CombineGVCFs {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = 1 + ceil(size(gvcfFiles, "G") * 8)
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -607,7 +607,7 @@ task DenoiseReadCounts {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = 5
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -665,7 +665,7 @@ task FilterMutectCalls {
String memory = "13G"
String javaXmx = "12G"
Int timeMinutes = 60
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -728,7 +728,7 @@ task GatherBqsrReports {
Int memoryMb = 256 + javaXmxMb
Int javaXmxMb = 256
Int timeMinutes = 1
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -774,7 +774,7 @@ task GenomicsDBImport {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = 180
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -833,7 +833,7 @@ task GenotypeGVCFs {
String memory = "7G"
String javaXmx = "6G"
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -899,7 +899,7 @@ task GetPileupSummaries {
String memory = "13G"
String javaXmx = "12G"
Int timeMinutes = 120
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -966,7 +966,7 @@ task HaplotypeCaller {
# Memory increases with time used. 4G should cover most use cases.
Int javaXmxMb = 4096
Int timeMinutes = 400 # This will likely be used with intervals, as such size based estimation can't be used.
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -1040,7 +1040,7 @@ task LearnReadOrientationModel {
String memory = "13G"
String javaXmx = "12G"
Int timeMinutes = 120
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -1079,7 +1079,7 @@ task MergeStats {
String memory = "15G"
String javaXmx = "14G"
Int timeMinutes = 30
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -1126,7 +1126,7 @@ task ModelSegments {
String memory = "11G"
String javaXmx = "10G"
Int timeMinutes = 60
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -1202,7 +1202,7 @@ task MuTect2 {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = 240
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -1389,7 +1389,7 @@ task PreprocessIntervals {
String memory = "4G"
String javaXmx = "3G"
Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 6)
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -1447,7 +1447,7 @@ task SelectVariants {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = 60
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -1507,7 +1507,7 @@ task SplitNCigarReads {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -1576,7 +1576,7 @@ task VariantEval {
String javaXmx = "4G"
# TODO: Refine estimate. For now 4 minutes per GB of input.
Int timeMinutes = ceil(size(flatten([evalVcfs, comparisonVcfs, select_all([referenceFasta, dbsnpVCF])]), "G") * 20)
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.7.0--py38_0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
@@ -1647,7 +1647,7 @@ task VariantFiltration {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = 120
- String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
+ String dockerImage = "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"
}
command {
--
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