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Commit 959bf985 authored by Ruben Vorderman's avatar Ruben Vorderman
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Update default gatk image

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gatk.wdl
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......@@ -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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