diff --git a/gatk.wdl b/gatk.wdl
index 31d895fd4e4cd9809b17b1935ed35ff0c8330a62..7964b519a413cb6535f2e0976f7fa4ab9d2280a2 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -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"
}
diff --git a/manta.wdl b/manta.wdl
index 5006a01efb5d92a97d527fa26b5866db959c3329..5382d2a5b6ad067efe9ba395ff7ab48077630f83 100644
--- a/manta.wdl
+++ b/manta.wdl
@@ -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"}
}
}
diff --git a/picard.wdl b/picard.wdl
index d19e3ac41e17370eec001a8df0f1c2a44e8c7c7e..494ccf98fc6903a8db5a4e1dd1617184bd5cab93 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -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"}
}
diff --git a/samtools.wdl b/samtools.wdl
index 5ffebc9ced931a1edba9022e2bb9df2fafb8d1c2..bdf811a04478824d98fd377a0cab7ddb0be6cf07 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -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"}
}
diff --git a/somaticseq.wdl b/somaticseq.wdl
index 49e5c36d4a5b388e596bcd2c943812f8011c3a57..7b9a4403c6e31c1ad6374b4561bfaee96dc4c435 100644
--- a/somaticseq.wdl
+++ b/somaticseq.wdl
@@ -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"}
}
diff --git a/strelka.wdl b/strelka.wdl
index 826cbd8e260014c1816d6640c313f3ebbb39bdef..50c38b55ae4374efc7ea32e7be8f6e08a0076cdb 100644
--- a/strelka.wdl
+++ b/strelka.wdl
@@ -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"}
}
diff --git a/vardict.wdl b/vardict.wdl
index 7bfd118ee99f67da1af482b240d1f9c6d34fe9f1..ffd05547e2e4acc2d7c81a16a04e1218ad6935c9 100644
--- a/vardict.wdl
+++ b/vardict.wdl
@@ -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"}
}