Commit e3569a58 authored by cagaser's avatar cagaser
Browse files

Merge remote-tracking branch 'origin/develop'

parents e1281833 70cb8bdc
......@@ -9,7 +9,7 @@ that users understand how the changes affect the new version.
-->
version 5.0.1
---------------------------
+ Update number of tasks: add memory runtime
+ add runtime memory to number of tasks.
version 5.0.0
---------------------------
......
......@@ -25,6 +25,7 @@ task BgzipAndIndex {
File inputFile
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
memory: memory
......@@ -55,6 +57,7 @@ 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"}
......
......@@ -47,6 +47,7 @@ task ParallelPaired {
File? strelkaSNV
File? strelkaIndel
String memory = "2G"
Int threads = 1
Int timeMinutes = 60
String memory = "2G"
......@@ -92,6 +93,7 @@ task ParallelPaired {
runtime {
cpu: threads
memory: memory
time_minutes: timeMinutes
memory: memory
docker: dockerImage
......@@ -123,6 +125,7 @@ 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"}
......@@ -161,6 +164,7 @@ task ParallelPairedTrain {
File? strelkaSNV
File? strelkaIndel
String memory = "2G"
Int threads = 1
Int timeMinutes = 240
String memory = "2G"
......@@ -205,6 +209,7 @@ task ParallelPairedTrain {
runtime {
cpu: threads
memory: memory
time_minutes: timeMinutes
memory: memory
docker: dockerImage
......@@ -236,6 +241,7 @@ 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"}
......@@ -268,6 +274,7 @@ task ParallelSingle {
File? scalpelVCF
File? strelkaVCF
String memory = "2G"
Int threads = 1
Int timeMinutes = 60
String memory = "2G"
......@@ -306,6 +313,7 @@ task ParallelSingle {
runtime {
cpu: threads
memory: memory
time_minutes: timeMinutes
memory: memory
docker: dockerImage
......@@ -329,6 +337,7 @@ 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"}
......@@ -359,6 +368,7 @@ task ParallelSingleTrain {
File? scalpelVCF
File? strelkaVCF
String memory = "2G"
Int threads = 1
Int timeMinutes = 240
String memory = "2G"
......@@ -396,6 +406,7 @@ task ParallelSingleTrain {
runtime {
cpu: threads
memory: memory
time_minutes: timeMinutes
memory: memory
docker: dockerImage
......@@ -419,6 +430,7 @@ 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"}
......@@ -437,6 +449,7 @@ task ModifyStrelka {
File strelkaVCF
String outputVCFName = basename(strelkaVCF, ".gz")
String memory = "2G"
Int timeMinutes = 20
String memory = "2G"
String dockerImage = "lethalfang/somaticseq:3.1.0"
......@@ -456,6 +469,7 @@ task ModifyStrelka {
}
runtime {
memory: memory
time_minutes: timeMinutes
memory: memory
docker: dockerImage
......@@ -465,6 +479,7 @@ 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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