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Unverified Commit a4a3de94 authored by Cedrick Agaser's avatar Cedrick Agaser Committed by GitHub
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Merge pull request #290 from biowdl/patch_tasks 

add runtime memory to number of tasks
parents 3a01f3b4 5cb91703
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CHANGELOG.md
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− 0
View file @ a4a3de94
......@@ -7,6 +7,9 @@ Newest changes should be on top.
This document is user facing. Please word the changes in such a way
that users understand how the changes affect the new version.
-->
version 5.0.1-dev
---------------------------
+ add runtime memory to number of tasks.
version 5.0.0
---------------------------
......
samtools.wdl
+ 3
− 0
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......@@ -26,6 +26,7 @@ task BgzipAndIndex {
String outputDir
String type = "vcf"
String memory = "2G"
Int timeMinutes = 1 + ceil(size(inputFile, "G"))
String dockerImage = "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
}
......@@ -45,6 +46,7 @@ task BgzipAndIndex {
}
runtime {
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -54,6 +56,7 @@ 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"}
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 @ a4a3de94
......@@ -47,6 +47,7 @@ task ParallelPaired {
File? strelkaSNV
File? strelkaIndel
String memory = "2G"
Int threads = 1
Int timeMinutes = 60
String dockerImage = "lethalfang/somaticseq:3.1.0"
......@@ -91,6 +92,7 @@ task ParallelPaired {
runtime {
cpu: threads
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -121,6 +123,7 @@ task ParallelPaired {
strelkaSNV: {description: "An SNV VCF as produced by strelka.", category: "advanced"}
strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", 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"}
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 {
File? strelkaSNV
File? strelkaIndel
String memory = "2G"
Int threads = 1
Int timeMinutes = 240
String dockerImage = "lethalfang/somaticseq:3.1.0"
......@@ -202,6 +206,7 @@ task ParallelPairedTrain {
runtime {
cpu: threads
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -232,6 +237,7 @@ task ParallelPairedTrain {
strelkaSNV: {description: "An SNV VCF as produced by strelka.", category: "advanced"}
strelkaIndel: {description: "An indel VCF as produced by somaticsniper.", 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"}
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 {
File? scalpelVCF
File? strelkaVCF
String memory = "2G"
Int threads = 1
Int timeMinutes = 60
String dockerImage = "lethalfang/somaticseq:3.1.0"
......@@ -301,6 +308,7 @@ task ParallelSingle {
runtime {
cpu: threads
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -323,6 +331,7 @@ task ParallelSingle {
scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"}
strelkaVCF: {description: "A VCF as produced by strelka.", 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"}
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 {
File? scalpelVCF
File? strelkaVCF
String memory = "2G"
Int threads = 1
Int timeMinutes = 240
String dockerImage = "lethalfang/somaticseq:3.1.0"
......@@ -389,6 +399,7 @@ task ParallelSingleTrain {
runtime {
cpu: threads
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -411,6 +422,7 @@ task ParallelSingleTrain {
scalpelVCF: {description: "A VCF as produced by scalpel.", category: "advanced"}
strelkaVCF: {description: "A VCF as produced by strelka.", 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"}
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 {
File strelkaVCF
String outputVCFName = basename(strelkaVCF, ".gz")
String memory = "2G"
Int timeMinutes = 20
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
......@@ -447,6 +460,7 @@ task ModifyStrelka {
}
runtime {
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
......@@ -455,6 +469,7 @@ task ModifyStrelka {
# inputs
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"}
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"}
......
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