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Commit 99b1586c authored by Cats's avatar Cats
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time_minutes

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gatk.wdl
+ 19
− 9
View file @ 99b1586c
......@@ -92,7 +92,7 @@ task ApplyBQSR {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can be used.
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"
}
......@@ -122,6 +122,7 @@ task ApplyBQSR {
runtime {
docker: dockerImage
time_minutes: timeMinutes
memory: memory
}
......@@ -163,7 +164,7 @@ task BaseRecalibrator {
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can be used.
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"
}
......@@ -413,15 +414,16 @@ task CombineGVCFs {
File referenceFastaDict
File referenceFastaFai
String memory = "24G"
String javaXmx = "12G"
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = ceil(size(gvcfFiles, "G") * 8)
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
gatk --java-options -Xmx~{javaXmx} \
gatk --java-options -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
CombineGVCFs \
-R ~{referenceFasta} \
-O ~{outputPath} \
......@@ -436,6 +438,7 @@ task CombineGVCFs {
runtime {
docker: dockerImage
time_minutes: timeMinutes
memory: memory
}
......@@ -453,6 +456,7 @@ task CombineGVCFs {
memory: {description: "The amount of memory this job will use.", category: "advanced"}
javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
}
......@@ -795,15 +799,16 @@ task GenotypeGVCFs {
File? dbsnpVCFIndex
File? pedigree
String memory = "18G"
String memory = "7G"
String javaXmx = "6G"
Int timeMinutes = 120 # This will likely be used with intervals, as such size based estimation can't be used.
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
gatk --java-options -Xmx~{javaXmx} \
gatk --java-options -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
GenotypeGVCFs \
-R ~{referenceFasta} \
-O ~{outputPath} \
......@@ -823,6 +828,7 @@ task GenotypeGVCFs {
runtime {
docker: dockerImage
time_minutes: timeMinutes
memory: memory
}
......@@ -843,6 +849,7 @@ task GenotypeGVCFs {
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"}
}
......@@ -919,15 +926,16 @@ task HaplotypeCaller {
Boolean gvcf = false
String emitRefConfidence = if gvcf then "GVCF" else "NONE"
String memory = "12G"
String memory = "5G"
String javaXmx = "4G"
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"
}
command {
set -e
mkdir -p "$(dirname ~{outputPath})"
gatk --java-options -Xmx~{javaXmx} \
gatk --java-options -Xmx~{javaXmx} -XX:ParallelGCThreads=1 \
HaplotypeCaller \
-R ~{referenceFasta} \
-O ~{outputPath} \
......@@ -949,6 +957,7 @@ task HaplotypeCaller {
runtime {
docker: dockerImage
time_minutes: timeMinutes
memory: memory
}
......@@ -976,6 +985,7 @@ task HaplotypeCaller {
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"}
}
......
picard.wdl
+ 5
− 2
View file @ 99b1586c
......@@ -489,8 +489,9 @@ task MergeVCFs {
Array[File]+ inputVCFsIndexes
String outputVcfPath
String memory = "24G"
String javaXmx = "8G"
String memory = "5G"
String javaXmx = "4G"
Int timeMinutes = size(inputVCFs, "G")
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
......@@ -513,6 +514,7 @@ task MergeVCFs {
runtime {
docker: dockerImage
time_minutes: timeMinutes
memory: memory
}
......@@ -525,6 +527,7 @@ task MergeVCFs {
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"}
}
......
umi-tools.wdl
+ 1
− 0
View file @ 99b1586c
......@@ -118,6 +118,7 @@ task Dedup {
umiSeparator: {description: "Seperator used for UMIs in the read names.", category: "advanced"}
paired: {description: "Whether or not the data is paired.", category: "common"}
memory: {description: "The amount of memory required for the task.", 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"}
}
......
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