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Commit 84ba1ef7 authored by Cats's avatar Cats
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time_minutes!

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gatk.wdl
+ 2
− 2
View file @ 84ba1ef7
......@@ -664,7 +664,7 @@ task FilterMutectCalls {
String memory = "16G"
String javaXmx = "12G"
Int timeMinutes = 180
Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
......@@ -1071,7 +1071,7 @@ task MergeStats {
String memory = "16G"
String javaXmx = "14G"
Int timeMinutes = 120
Int timeMinutes = 30
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
......
manta.wdl
+ 6
− 0
View file @ 84ba1ef7
......@@ -33,6 +33,7 @@ task Germline {
Int cores = 1
Int memoryGb = 4
Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
}
......@@ -60,6 +61,7 @@ task Germline {
cpu: cores
memory: "~{memoryGb}G"
docker: dockerImage
time_minutes: timeMinutes
}
parameter_meta {
......@@ -74,6 +76,7 @@ task Germline {
exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
cores: {description: "The the number of cores required to run a program", category: "required"}
memoryGb: {description: "The memory required to run the manta", category: "required"}
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"}
}
}
......@@ -93,6 +96,7 @@ task Somatic {
Int cores = 1
Int memoryGb = 4
Int timeMinutes = 60
String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
}
......@@ -130,6 +134,7 @@ task Somatic {
cpu: cores
memory: "~{memoryGb}G"
docker: dockerImage
time_minutes: timeMinutes
}
parameter_meta {
......@@ -145,6 +150,7 @@ task Somatic {
exome: {description: "Whether or not the data is from exome sequencing.", category: "common"}
cores: {description: "The number of cores to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in Gigabytes.", 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
+ 4
− 1
View file @ 84ba1ef7
......@@ -619,8 +619,9 @@ task SortVcf {
String outputVcfPath
File? dict
String memory = "24G"
String memory = "10G"
String javaXmx = "8G"
Int timeMinutes = 1 + ceil(size(vcfFiles, "G") * 5)
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
......@@ -642,6 +643,7 @@ task SortVcf {
runtime {
docker: dockerImage
time_minutes: timeMinutes
memory: memory
}
......@@ -654,6 +656,7 @@ task SortVcf {
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"}
}
......
samtools.wdl
+ 7
− 1
View file @ 84ba1ef7
......@@ -26,6 +26,7 @@ task BgzipAndIndex {
String outputDir
String type = "vcf"
Int timeMinutes = 1 + ceil(size(inputFile, "G"))
String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
}
......@@ -44,7 +45,8 @@ task BgzipAndIndex {
}
runtime {
docker: dockerImage
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
......@@ -52,6 +54,7 @@ task BgzipAndIndex {
inputFile: {description: "The file to be compressed and indexed.", category: "required"}
outputDir: {description: "The directory in which the output will be placed.", category: "required"}
type: {description: "The type of file (eg. vcf or bed) to be compressed and indexed.", category: "common"}
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"}
}
......@@ -395,6 +398,7 @@ task View {
Int threads = 1
String memory = "1G"
Int timeMinutes = 1 + ceil(size(inFile, "G") * 5)
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
String outputIndexPath = basename(outputFileName) + ".bai"
......@@ -424,6 +428,7 @@ task View {
runtime {
cpu: threads
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -440,6 +445,7 @@ task View {
threads: {description: "The number of threads to use.", category: "advanced"}
memory: {description: "The amount of memory this job will use.", 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"}
}
......
somaticseq.wdl
+ 15
− 0
View file @ 84ba1ef7
......@@ -47,6 +47,7 @@ task ParallelPaired {
File? strelkaIndel
Int threads = 1
Int timeMinutes = 60
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
......@@ -89,6 +90,7 @@ task ParallelPaired {
runtime {
cpu: threads
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -118,6 +120,7 @@ task ParallelPaired {
strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", category: "advanced"}
threads: {description: "The number of threads to use.", 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"}
}
......@@ -150,6 +153,7 @@ task ParallelPairedTrain {
File? strelkaIndel
Int threads = 1
Int timeMinutes = 240
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
......@@ -191,6 +195,7 @@ task ParallelPairedTrain {
runtime {
cpu: threads
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -220,6 +225,7 @@ task ParallelPairedTrain {
strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", category: "advanced"}
threads: {description: "The number of threads to use.", 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"}
}
......@@ -244,6 +250,7 @@ task ParallelSingle {
File? strelkaVCF
Int threads = 1
Int timeMinutes = 60
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
......@@ -279,6 +286,7 @@ task ParallelSingle {
runtime {
cpu: threads
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -300,6 +308,7 @@ task ParallelSingle {
strelkaVCF: {description: "A VCF as produced by strelka.", category: "advanced"}
threads: {description: "The number of threads to use.", 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"}
}
......@@ -324,6 +333,7 @@ task ParallelSingleTrain {
File? strelkaVCF
Int threads = 1
Int timeMinutes = 240
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
......@@ -358,6 +368,7 @@ task ParallelSingleTrain {
runtime {
cpu: threads
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -379,6 +390,7 @@ task ParallelSingleTrain {
strelkaVCF: {description: "A VCF as produced by strelka.", category: "advanced"}
threads: {description: "The number of threads to use.", 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"}
}
......@@ -389,6 +401,7 @@ task ModifyStrelka {
File strelkaVCF
String outputVCFName = basename(strelkaVCF, ".gz")
String dockerImage = "lethalfang/somaticseq:3.1.0"
Int timeMinutes = 20
}
command {
......@@ -407,12 +420,14 @@ task ModifyStrelka {
}
runtime {
time_minutes: timeMinutes
docker: dockerImage
}
parameter_meta {
strelkaVCF: {description: "A vcf file as produced by strelka.", category: "required"}
outputVCFName: {description: "The location the output VCF file should be written to.", 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"}
}
......
strelka.wdl
+ 6
− 0
View file @ 84ba1ef7
......@@ -36,6 +36,7 @@ task Germline {
Int cores = 1
Int memoryGb = 4
Int timeMinutes = 90
String dockerImage = "quay.io/biocontainers/strelka:2.9.7--0"
}
......@@ -62,6 +63,7 @@ task Germline {
runtime {
docker: dockerImage
cpu: cores
time_minutes: timeMinutes
memory: "~{memoryGb}G"
}
......@@ -78,6 +80,7 @@ task Germline {
cores: {description: "The number of cores to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in Gigabytes.", 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"}
}
......@@ -100,6 +103,7 @@ task Somatic {
Int cores = 1
Int memoryGb = 4
Int timeMinutes = 90
String dockerImage = "quay.io/biocontainers/strelka:2.9.7--0"
File? doNotDefineThis #FIXME
......@@ -131,6 +135,7 @@ task Somatic {
runtime {
docker: dockerImage
cpu: cores
time_minutes: timeMinutes
memory: "~{memoryGb}G"
}
......@@ -150,6 +155,7 @@ task Somatic {
cores: {description: "The number of cores to use.", category: "advanced"}
memoryGb: {description: "The amount of memory this job will use in Gigabytes.", 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"}
}
......
vardict.wdl
+ 4
− 1
View file @ 84ba1ef7
......@@ -48,8 +48,9 @@ task VarDict {
Float minimumAlleleFrequency = 0.02
Int threads = 1
String memory = "40G"
String memory = "20G"
String javaXmx = "16G"
Int timeMinutes = 300
String dockerImage = "quay.io/biocontainers/vardict-java:1.5.8--1"
}
......@@ -87,6 +88,7 @@ task VarDict {
runtime {
cpu: threads + 2
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -116,6 +118,7 @@ task VarDict {
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"}
}
......
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