diff --git a/gatk.wdl b/gatk.wdl
index e6b86eed3d98c4444906d5d484cf4b8b02287e00..31d895fd4e4cd9809b17b1935ed35ff0c8330a62 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -34,6 +34,7 @@ task AnnotateIntervals {
String memory = "10G"
String javaXmx = "2G"
+ Int timeMinutes = 5
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -57,6 +58,7 @@ task AnnotateIntervals {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -73,6 +75,7 @@ task AnnotateIntervals {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -223,6 +226,7 @@ task CalculateContamination {
String memory = "24G"
String javaXmx = "12G"
+ Int timeMinutes = 180
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
@@ -243,6 +247,7 @@ task CalculateContamination {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -252,6 +257,7 @@ task CalculateContamination {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -262,8 +268,9 @@ task CallCopyRatioSegments {
String outputPrefix
File copyRatioSegments
- String memory = "21G"
- String javaXmx = "6G"
+ String memory = "3G"
+ String javaXmx = "2G"
+ Int timeMinutes = 2
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -283,6 +290,7 @@ task CallCopyRatioSegments {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -292,6 +300,7 @@ task CallCopyRatioSegments {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -307,8 +316,10 @@ task CollectAllelicCounts {
File referenceFasta
File referenceFastaDict
File referenceFastaFai
- String memory = "90G"
- String javaXmx = "30G"
+
+ String memory = "12G"
+ String javaXmx = "10G"
+ Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -329,6 +340,7 @@ task CollectAllelicCounts {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -344,6 +356,7 @@ task CollectAllelicCounts {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -360,8 +373,9 @@ task CollectReadCounts {
File referenceFastaFai
String intervalMergingRule = "OVERLAPPING_ONLY"
- String memory = "35G"
- String javaXmx = "7G"
+ String memory = "5G"
+ String javaXmx = "4G"
+ Int timeMinutes = 1 + ceil(size(inputBam, "G") * 5)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -384,6 +398,7 @@ task CollectReadCounts {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -399,6 +414,7 @@ task CollectReadCounts {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -474,8 +490,9 @@ task CombineVariants {
Array[File]+ variantIndexes
String outputPath
- String memory = "24G"
+ String memory = "16G"
String javaXmx = "12G"
+ Int timeMinutes = 180
String dockerImage = "broadinstitute/gatk3:3.8-1"
}
@@ -510,6 +527,7 @@ task CombineVariants {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -527,6 +545,7 @@ task CombineVariants {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -538,8 +557,9 @@ task CreateReadCountPanelOfNormals {
Array[File]+ readCountsFiles
File? annotatedIntervals
- String memory = "21G"
- String javaXmx = "7G"
+ String memory = "5G"
+ String javaXmx = "4G"
+ Int timeMinutes = 5
String dockerImage = "broadinstitute/gatk:4.1.4.0" # The biocontainer causes a spark related error for some reason...
}
@@ -559,6 +579,7 @@ task CreateReadCountPanelOfNormals {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -570,6 +591,7 @@ task CreateReadCountPanelOfNormals {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -582,8 +604,9 @@ task DenoiseReadCounts {
File readCounts
String outputPrefix
- String memory = "39G"
- String javaXmx = "13G"
+ String memory = "6G"
+ String javaXmx = "4G"
+ Int timeMinutes = 5
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -606,6 +629,7 @@ task DenoiseReadCounts {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -618,6 +642,7 @@ task DenoiseReadCounts {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -637,8 +662,9 @@ task FilterMutectCalls {
Int uniqueAltReadCount = 4
File mutect2Stats
- String memory = "24G"
+ String memory = "16G"
String javaXmx = "12G"
+ Int timeMinutes = 180
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
@@ -667,6 +693,7 @@ task FilterMutectCalls {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -686,6 +713,7 @@ task FilterMutectCalls {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -743,8 +771,9 @@ task GenomicsDBImport {
String genomicsDBWorkspacePath = "genomics_db"
String genomicsDBTarFile = "genomics_db.tar.gz"
String? tmpDir
- String memory = "12G"
+ String memory = "6G"
String javaXmx = "4G"
+ Int timeMinutes = 180
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -766,6 +795,7 @@ task GenomicsDBImport {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -780,6 +810,7 @@ task GenomicsDBImport {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -865,8 +896,9 @@ task GetPileupSummaries {
File sitesForContaminationIndex
String outputPrefix
- String memory = "24G"
+ String memory = "16G"
String javaXmx = "12G"
+ Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
@@ -886,6 +918,7 @@ task GetPileupSummaries {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -901,6 +934,7 @@ task GetPileupSummaries {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -996,8 +1030,9 @@ task LearnReadOrientationModel {
input {
Array[File]+ f1r2TarGz
- String memory = "24G"
+ String memory = "16G"
String javaXmx = "12G"
+ Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
@@ -1015,6 +1050,7 @@ task LearnReadOrientationModel {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1023,6 +1059,7 @@ task LearnReadOrientationModel {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1032,8 +1069,9 @@ task MergeStats {
input {
Array[File]+ stats
- String memory = "28G"
+ String memory = "16G"
String javaXmx = "14G"
+ Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -1051,6 +1089,7 @@ task MergeStats {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1059,6 +1098,7 @@ task MergeStats {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1076,8 +1116,9 @@ task ModelSegments {
else 30
Int maximumNumberOfSmoothingIterations = 10
- String memory = "64G"
+ String memory = "12G"
String javaXmx = "10G"
+ Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -1111,6 +1152,7 @@ task ModelSegments {
runtime {
docker: dockerImage
+ time_minute: timeMinutes
memory: memory
}
@@ -1126,6 +1168,7 @@ task ModelSegments {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1149,8 +1192,9 @@ task MuTect2 {
Array[File]+ intervals
String outputStats = outputVcf + ".stats"
- String memory = "16G"
+ String memory = "6G"
String javaXmx = "4G"
+ Int timeMinutes = 240
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -1179,6 +1223,7 @@ task MuTect2 {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1201,6 +1246,7 @@ task MuTect2 {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1215,8 +1261,9 @@ task PlotDenoisedCopyRatios {
File denoisedCopyRatios
Int? minimumContigLength
- String memory = "32G"
- String javaXmx = "7G"
+ String memory = "6G"
+ String javaXmx = "4G"
+ Int timeMinutes = 2
String dockerImage = "broadinstitute/gatk:4.1.4.0" # The biocontainer doesn't seem to contain R.
}
@@ -1244,6 +1291,7 @@ task PlotDenoisedCopyRatios {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1257,6 +1305,7 @@ task PlotDenoisedCopyRatios {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1272,8 +1321,9 @@ task PlotModeledSegments {
File allelicCounts
Int? minimumContigLength
- String memory = "21G"
- String javaXmx = "7G"
+ String memory = "6G"
+ String javaXmx = "4G"
+ Int timeMinutes = 2
String dockerImage = "broadinstitute/gatk:4.1.4.0" # The biocontainer doesn't seem to contain R.
}
@@ -1297,6 +1347,7 @@ task PlotModeledSegments {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1311,6 +1362,7 @@ task PlotModeledSegments {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1327,8 +1379,9 @@ task PreprocessIntervals {
Int padding = if defined(intervals) then 250 else 0
String intervalMergingRule = "OVERLAPPING_ONLY"
- String memory = "10G"
- String javaXmx = "2G"
+ String memory = "6G"
+ String javaXmx = "5G"
+ Int timeMinutes = 1 + ceil(size(referenceFasta, "G") * 6)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -1352,6 +1405,7 @@ task PreprocessIntervals {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1367,6 +1421,7 @@ task PreprocessIntervals {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1382,8 +1437,9 @@ task SelectVariants {
String outputPath = "output.vcf.gz"
String? selectTypeToInclude
Array[File] intervals = []
- String memory = "16G"
+ String memory = "6G"
String javaXmx = "4G"
+ Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -1406,6 +1462,7 @@ task SelectVariants {
runtime {
docker: dockerImage
+ time_minute: timeMinutes
memory: memory
}
@@ -1424,6 +1481,7 @@ task SelectVariants {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
@@ -1498,8 +1556,9 @@ task VariantFiltration {
Array[String]+ filterArguments
Array[File] intervals = []
- String memory = "16G"
+ String memory = "6G"
String javaXmx = "4G"
+ Int timeMinutes = 120
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
@@ -1522,6 +1581,7 @@ task VariantFiltration {
runtime {
docker: dockerImage
+ time_minutes: timeMinutes
memory: memory
}
@@ -1540,6 +1600,7 @@ task VariantFiltration {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
+ timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
diff --git a/umi-tools.wdl b/umi-tools.wdl
index 608924f3fdd8dc7f5592e54f9cddadc7044c9039..bd09853a949e33a1d8ea6d0ec81279e96600bb6d 100644
--- a/umi-tools.wdl
+++ b/umi-tools.wdl
@@ -75,8 +75,8 @@ task Dedup {
String? statsPrefix
Boolean paired = true
- String memory = "5G"
- Int timeMinutes = 1 + ceil(size(inputBam, "G") * 18)
+ String memory = "20G"
+ Int timeMinutes = 600 + ceil(size(inputBam, "G") * 60)
# Use a multi-package-container which includes umi_tools (0.5.5) and samtools (1.9)
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:6089936aca6219b5bb5f54210ac5eb456c7503f2-0"