From c9c36cf805cb70e488136609d99f601b16b1aa66 Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Tue, 20 Jul 2021 16:39:50 +0200
Subject: [PATCH] update samtools.wdl somaticseq.wdl: add memory runtime
---
samtools.wdl | 3 +++
somaticseq.wdl | 15 +++++++++++++++
2 files changed, 18 insertions(+)
diff --git a/samtools.wdl b/samtools.wdl
index 46d1eb7..81b6c17 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -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"}
diff --git a/somaticseq.wdl b/somaticseq.wdl
index 07103ef..2992a80 100644
--- a/somaticseq.wdl
+++ b/somaticseq.wdl
@@ -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"}
+ ParallelPaired
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"}
--
GitLab