Unverified Commit 9a7e49fb authored by Cedrick Agaser's avatar Cedrick Agaser Committed by GitHub
Browse files

Merge pull request #289 from biowdl/add_runtime_memory

Add runtime memory
parents 9b0873ab b287b608
......@@ -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
---------------------------
+ Update number of tasks: add memory runtime
version 5.0.0
---------------------------
......
......@@ -24,6 +24,8 @@ task AppendToStringArray {
input {
Array[String] array
String string
String memory = "1G"
}
command {
......@@ -36,7 +38,7 @@ task AppendToStringArray {
}
runtime {
memory: "1G"
memory: memory
}
}
......@@ -45,9 +47,11 @@ task CheckFileMD5 {
input {
File file
String md5
# By default cromwell expects /bin/bash to be present in the container.
# The 'bash' container does not fill this requirement. (It is in /usr/local/bin/bash)
# Use a stable version of debian:stretch-slim for this. (Smaller than ubuntu)
String memory = "1G"
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
......@@ -60,6 +64,7 @@ task CheckFileMD5 {
runtime {
docker: dockerImage
memory: memory
}
}
......@@ -69,6 +74,8 @@ task ConcatenateTextFiles {
String combinedFilePath
Boolean unzip = false
Boolean zip = false
String memory = "1G"
}
# When input and output is both compressed decompression is not needed.
......@@ -86,7 +93,7 @@ task ConcatenateTextFiles {
}
runtime {
memory: "1G"
memory: memory
}
}
......@@ -97,6 +104,7 @@ task Copy {
Boolean recursive = false
# Version not that important as long as it is stable.
String memory = "1G"
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
......@@ -112,6 +120,7 @@ task Copy {
runtime {
docker: dockerImage
memory: memory
}
}
......@@ -122,6 +131,8 @@ task CreateLink {
input {
String inputFile
String outputPath
String memory = "1G"
}
command {
......@@ -131,12 +142,17 @@ task CreateLink {
output {
File link = outputPath
}
runtime {
memory: memory
}
}
task MapMd5 {
input {
Map[String,String] map
String memory = "1G"
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
......@@ -150,7 +166,7 @@ task MapMd5 {
}
runtime {
memory: "1G"
memory: memory
docker: dockerImage
}
}
......@@ -160,6 +176,7 @@ task StringArrayMd5 {
input {
Array[String] stringArray
String memory = "1G"
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
......@@ -173,7 +190,7 @@ task StringArrayMd5 {
}
runtime {
memory: "1G"
memory: memory
docker: dockerImage
}
}
......@@ -183,6 +200,7 @@ task TextToFile {
String text
String outputFile = "out.txt"
String memory = "1G"
Int timeMinutes = 1
String dockerImage = "debian@sha256:f05c05a218b7a4a5fe979045b1c8e2a9ec3524e5611ebfdd0ef5b8040f9008fa"
}
......@@ -196,7 +214,7 @@ task TextToFile {
}
runtime {
memory: "1G"
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
......
......@@ -143,6 +143,7 @@ task Fastqc {
task GetConfiguration {
input {
String memory = "2G" # Needs more than 1 to pull the docker image.
Int timeMinutes = 1
String dockerImage = "quay.io/biocontainers/fastqc:0.11.7--4"
}
......@@ -165,7 +166,7 @@ task GetConfiguration {
}
runtime {
memory: "2G" # Needs more than 1 to pull the docker image.
memory: memory
time_minute: timeMinutes
docker: dockerImage
}
......@@ -173,6 +174,7 @@ task GetConfiguration {
parameter_meta {
# inputs
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
memory: {description: "The amount of memory available to the job.", 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"}
# outputs
......
......@@ -25,7 +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"
}
......@@ -47,6 +47,7 @@ task BgzipAndIndex {
runtime {
time_minutes: timeMinutes
docker: dockerImage
memory: memory
}
parameter_meta {
......
......@@ -49,6 +49,7 @@ task ParallelPaired {
Int threads = 1
Int timeMinutes = 60
String memory = "2G"
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
......@@ -92,6 +93,7 @@ task ParallelPaired {
runtime {
cpu: threads
time_minutes: timeMinutes
memory: memory
docker: dockerImage
}
......@@ -161,6 +163,7 @@ task ParallelPairedTrain {
Int threads = 1
Int timeMinutes = 240
String memory = "2G"
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
......@@ -203,6 +206,7 @@ task ParallelPairedTrain {
runtime {
cpu: threads
time_minutes: timeMinutes
memory: memory
docker: dockerImage
}
......@@ -266,6 +270,7 @@ task ParallelSingle {
Int threads = 1
Int timeMinutes = 60
String memory = "2G"
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
......@@ -302,6 +307,7 @@ task ParallelSingle {
runtime {
cpu: threads
time_minutes: timeMinutes
memory: memory
docker: dockerImage
}
......@@ -355,6 +361,7 @@ task ParallelSingleTrain {
Int threads = 1
Int timeMinutes = 240
String memory = "2G"
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
......@@ -390,6 +397,7 @@ task ParallelSingleTrain {
runtime {
cpu: threads
time_minutes: timeMinutes
memory: memory
docker: dockerImage
}
......@@ -430,6 +438,7 @@ task ModifyStrelka {
String outputVCFName = basename(strelkaVCF, ".gz")
Int timeMinutes = 20
String memory = "2G"
String dockerImage = "lethalfang/somaticseq:3.1.0"
}
......@@ -448,6 +457,7 @@ task ModifyStrelka {
runtime {
time_minutes: timeMinutes
memory: memory
docker: dockerImage
}
......
......@@ -30,6 +30,7 @@ task Extract {
String? read2Output = "umi_extracted_R2.fastq.gz"
Boolean threePrime = false
String memory = "20G"
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 2)
String dockerImage = "quay.io/biocontainers/mulled-v2-509311a44630c01d9cb7d2ac5727725f51ea43af:3067b520386698317fd507c413baf7f901666fd4-0"
}
......@@ -51,6 +52,7 @@ task Extract {
}
runtime {
memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
......
......@@ -31,6 +31,7 @@ task Count {
Int? binSize
File? binFile
String memory = "2G"
String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
}
......@@ -50,6 +51,7 @@ task Count {
}
runtime {
memory: memory
docker: dockerImage
}
}
......@@ -67,6 +69,7 @@ task GcCorrect {
Int? iter
Float? fracLowess
String memory = "2G"
String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
}
......@@ -89,6 +92,7 @@ task GcCorrect {
}
runtime {
memory: memory
docker: dockerImage
}
}
......@@ -143,6 +147,7 @@ task Zscore {
Int? binSize
File? binFile
String memory = "2G"
String dockerImage = "quay.io/biocontainers/wisestork:0.1.2--pyh24bf2e0_0"
}
......@@ -163,6 +168,7 @@ task Zscore {
}
runtime {
memory: memory
docker: dockerImage
}
}
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