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Commit c9c36cf8 authored by cagaser's avatar cagaser
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update samtools.wdl somaticseq.wdl: add memory runtime

parent 3a01f3b4
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samtools.wdl
+ 3
− 0
View file @ c9c36cf8
...@@ -26,6 +26,7 @@ task BgzipAndIndex { ...@@ -26,6 +26,7 @@ task BgzipAndIndex {
String outputDir String outputDir
String type = "vcf" String type = "vcf"
String memory = "2G"
Int timeMinutes = 1 + ceil(size(inputFile, "G")) Int timeMinutes = 1 + ceil(size(inputFile, "G"))
String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0" String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
} }
...@@ -45,6 +46,7 @@ task BgzipAndIndex { ...@@ -45,6 +46,7 @@ task BgzipAndIndex {
} }
runtime { runtime {
memory: memory
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -54,6 +56,7 @@ task BgzipAndIndex { ...@@ -54,6 +56,7 @@ task BgzipAndIndex {
inputFile: {description: "The file to be compressed and indexed.", category: "required"} inputFile: {description: "The file to be compressed and indexed.", category: "required"}
outputDir: {description: "The directory in which the output will be placed.", 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"} type: {description: "The type of file (eg. vcf or bed) to be compressed and indexed.", category: "common"}
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"} 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"} 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 @ c9c36cf8
...@@ -47,6 +47,7 @@ task ParallelPaired { ...@@ -47,6 +47,7 @@ task ParallelPaired {
File? strelkaSNV File? strelkaSNV
File? strelkaIndel File? strelkaIndel
String memory = "2G"
Int threads = 1 Int threads = 1
Int timeMinutes = 60 Int timeMinutes = 60
String dockerImage = "lethalfang/somaticseq:3.1.0" String dockerImage = "lethalfang/somaticseq:3.1.0"
...@@ -91,6 +92,7 @@ task ParallelPaired { ...@@ -91,6 +92,7 @@ task ParallelPaired {
runtime { runtime {
cpu: threads cpu: threads
memory: memory
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -121,6 +123,7 @@ task ParallelPaired { ...@@ -121,6 +123,7 @@ task ParallelPaired {
strelkaSNV: {description: "An SNV VCF as produced by strelka.", category: "advanced"} strelkaSNV: {description: "An SNV VCF as produced by strelka.", category: "advanced"}
strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", category: "advanced"} strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"} threads: {description: "The number of threads to use.", category: "advanced"}
ParallelPaired
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", 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"} 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"}
...@@ -159,6 +162,7 @@ task ParallelPairedTrain { ...@@ -159,6 +162,7 @@ task ParallelPairedTrain {
File? strelkaSNV File? strelkaSNV
File? strelkaIndel File? strelkaIndel
String memory = "2G"
Int threads = 1 Int threads = 1
Int timeMinutes = 240 Int timeMinutes = 240
String dockerImage = "lethalfang/somaticseq:3.1.0" String dockerImage = "lethalfang/somaticseq:3.1.0"
...@@ -202,6 +206,7 @@ task ParallelPairedTrain { ...@@ -202,6 +206,7 @@ task ParallelPairedTrain {
runtime { runtime {
cpu: threads cpu: threads
memory: memory
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -232,6 +237,7 @@ task ParallelPairedTrain { ...@@ -232,6 +237,7 @@ task ParallelPairedTrain {
strelkaSNV: {description: "An SNV VCF as produced by strelka.", category: "advanced"} strelkaSNV: {description: "An SNV VCF as produced by strelka.", category: "advanced"}
strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", category: "advanced"} strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"} 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"} 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"} 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"}
...@@ -264,6 +270,7 @@ task ParallelSingle { ...@@ -264,6 +270,7 @@ task ParallelSingle {
File? scalpelVCF File? scalpelVCF
File? strelkaVCF File? strelkaVCF
String memory = "2G"
Int threads = 1 Int threads = 1
Int timeMinutes = 60 Int timeMinutes = 60
String dockerImage = "lethalfang/somaticseq:3.1.0" String dockerImage = "lethalfang/somaticseq:3.1.0"
...@@ -301,6 +308,7 @@ task ParallelSingle { ...@@ -301,6 +308,7 @@ task ParallelSingle {
runtime { runtime {
cpu: threads cpu: threads
memory: memory
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -323,6 +331,7 @@ task ParallelSingle { ...@@ -323,6 +331,7 @@ task ParallelSingle {
scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"} scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"}
strelkaVCF: {description: "A VCF as produced by strelka.", category: "advanced"} strelkaVCF: {description: "A VCF as produced by strelka.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"} 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"} 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"} 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"}
...@@ -353,6 +362,7 @@ task ParallelSingleTrain { ...@@ -353,6 +362,7 @@ task ParallelSingleTrain {
File? scalpelVCF File? scalpelVCF
File? strelkaVCF File? strelkaVCF
String memory = "2G"
Int threads = 1 Int threads = 1
Int timeMinutes = 240 Int timeMinutes = 240
String dockerImage = "lethalfang/somaticseq:3.1.0" String dockerImage = "lethalfang/somaticseq:3.1.0"
...@@ -389,6 +399,7 @@ task ParallelSingleTrain { ...@@ -389,6 +399,7 @@ task ParallelSingleTrain {
runtime { runtime {
cpu: threads cpu: threads
memory: memory
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -411,6 +422,7 @@ task ParallelSingleTrain { ...@@ -411,6 +422,7 @@ task ParallelSingleTrain {
scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"} scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"}
strelkaVCF: {description: "A VCF as produced by strelka.", category: "advanced"} strelkaVCF: {description: "A VCF as produced by strelka.", category: "advanced"}
threads: {description: "The number of threads to use.", category: "advanced"} 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"} 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"} 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"}
...@@ -429,6 +441,7 @@ task ModifyStrelka { ...@@ -429,6 +441,7 @@ task ModifyStrelka {
File strelkaVCF File strelkaVCF
String outputVCFName = basename(strelkaVCF, ".gz") String outputVCFName = basename(strelkaVCF, ".gz")
String memory = "2G"
Int timeMinutes = 20 Int timeMinutes = 20
String dockerImage = "lethalfang/somaticseq:3.1.0" String dockerImage = "lethalfang/somaticseq:3.1.0"
} }
...@@ -447,6 +460,7 @@ task ModifyStrelka { ...@@ -447,6 +460,7 @@ task ModifyStrelka {
} }
runtime { runtime {
memory: memory
time_minutes: timeMinutes time_minutes: timeMinutes
docker: dockerImage docker: dockerImage
} }
...@@ -455,6 +469,7 @@ task ModifyStrelka { ...@@ -455,6 +469,7 @@ task ModifyStrelka {
# inputs # inputs
strelkaVCF: {description: "A vcf file as produced by strelka.", category: "required"} 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"} outputVCFName: {description: "The location the output VCF file should be written to.", 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"} 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"} 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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