From 401808be277bc6991d92897678039e711abed668 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 2 Oct 2019 13:38:04 +0200
Subject: [PATCH] memory Int -> String part 3
---
biopet/bamstats.wdl | 10 +++++-----
biopet/biopet.wdl | 20 ++++++++++----------
biopet/sampleconfig.wdl | 30 +++++++++++++++---------------
biopet/seqstat.wdl | 10 +++++-----
centrifuge.wdl | 6 +++---
collect-columns.wdl | 4 ++--
flash.wdl | 2 +-
stringtie.wdl | 2 +-
8 files changed, 42 insertions(+), 42 deletions(-)
diff --git a/biopet/bamstats.wdl b/biopet/bamstats.wdl
index d5a30f0..a00ed97 100644
--- a/biopet/bamstats.wdl
+++ b/biopet/bamstats.wdl
@@ -16,15 +16,15 @@ task Generate {
String outputDir
Reference? reference
- Int memory = 8
- Float memoryMultiplier = 2.0
+ String memory = "16G"
+ String javaXmx = "8G"
}
File referenceFasta = if defined(reference) then select_first([reference]).fasta else ""
String toolCommand = if defined(toolJar)
- then "java -Xmx" + memory + "G -jar " + toolJar
- else "biopet-bamstats -Xmx" + memory + "G"
+ then "java -Xmx~{javaXmx} -jar " + toolJar
+ else "biopet-bamstats -Xmx~{javaXmx}"
command {
set -e -o pipefail
@@ -46,6 +46,6 @@ task Generate {
}
runtime {
- memory: ceil(memory * memoryMultiplier)
+ memory: memory
}
}
\ No newline at end of file
diff --git a/biopet/biopet.wdl b/biopet/biopet.wdl
index 92f38ef..8cf2381 100644
--- a/biopet/biopet.wdl
+++ b/biopet/biopet.wdl
@@ -11,13 +11,13 @@ task BaseCounter {
String outputDir
String prefix
- Int memory = 4
- Float memoryMultiplier = 3.5
+ String memory = "14G"
+ String javaXmx = "4G"
}
String toolCommand = if defined(toolJar)
- then "java -Xmx" + memory + "G -jar " +toolJar
- else "biopet-basecounter -Xmx" + memory + "G"
+ then "java -Xmx~{javaXmx} -jar " + toolJar
+ else "biopet-basecounter -Xmx~{javaXmx}"
command {
set -e -o pipefail
@@ -68,7 +68,7 @@ task BaseCounter {
}
runtime {
- memory: ceil(memory * memoryMultiplier)
+ memory: memory
}
}
@@ -155,13 +155,13 @@ task FastqSync {
String out2path
File? toolJar
- Int memory = 4
- Float memoryMultiplier = 2.5
+ String memory = "10G"
+ String javaXmx = "4G"
}
String toolCommand = if defined(toolJar)
- then "java -Xmx" + memory + "G -jar " +toolJar
- else "biopet-fastqsync -Xmx" + memory + "G"
+ then "java -Xmx~{javaXmx} -jar " + toolJar
+ else "biopet-fastqsync -Xmx~{javaXmx}"
command {
set -e -o pipefail
@@ -184,7 +184,7 @@ task FastqSync {
}
runtime {
- memory: ceil(memory * memoryMultiplier)
+ memory: memory
}
}
diff --git a/biopet/sampleconfig.wdl b/biopet/sampleconfig.wdl
index 321b77c..59f0bad 100644
--- a/biopet/sampleconfig.wdl
+++ b/biopet/sampleconfig.wdl
@@ -14,13 +14,13 @@ task SampleConfig {
String? jsonOutputPath
String? tsvOutputPath
- Int memory = 4
- Float memoryMultiplier = 2.0
+ String memory = "8G"
+ String javaXmx = "16G"
}
String toolCommand = if defined(toolJar)
- then "java -Xmx" + memory + "G -jar " +toolJar
- else "biopet-sampleconfig -Xmx" + memory + "G"
+ then "java -Xmx~{javaXmx} -jar " + toolJar
+ else "biopet-sampleconfig -Xmx~{javaXmx}"
command {
set -e -o pipefail
@@ -43,7 +43,7 @@ task SampleConfig {
}
runtime {
- memory: ceil(memory * memoryMultiplier)
+ memory: memory
}
}
@@ -54,13 +54,13 @@ task SampleConfigCromwellArrays {
Array[File]+ inputFiles
String outputPath
- Int memory = 4
- Float memoryMultiplier = 2.0
+ String memory = "8G"
+ String javaXmx = "4G"
}
String toolCommand = if defined(toolJar)
- then "java -Xmx" + memory + "G -jar " + toolJar
- else "biopet-sampleconfig -Xmx" + memory + "G"
+ then "java -Xmx~{javaXmx} -jar " + toolJar
+ else "biopet-sampleconfig -Xmx~{javaXmx}"
command {
set -e -o pipefail
@@ -76,7 +76,7 @@ task SampleConfigCromwellArrays {
}
runtime {
- memory: ceil(memory * memoryMultiplier)
+ memory: memory
}
}
@@ -90,13 +90,13 @@ task CaseControl {
String outputPath
String controlTag = "control"
- Int memory = 4
- Float memoryMultiplier = 2.0
+ String memory = "8G"
+ String javaXmx = "4G"
}
String toolCommand = if defined(toolJar)
- then "java -Xmx" + memory + "G -jar " + toolJar
- else "biopet-sampleconfig -Xmx" + memory + "G"
+ then "java -Xmx~{javaXmx} -jar " + toolJar
+ else "biopet-sampleconfig -Xmx~{javaXmx}"
command {
set -e -o pipefail
@@ -115,6 +115,6 @@ task CaseControl {
}
runtime {
- memory: ceil(memory * memoryMultiplier)
+ memory: memory
}
}
diff --git a/biopet/seqstat.wdl b/biopet/seqstat.wdl
index c8b591f..ade4b45 100644
--- a/biopet/seqstat.wdl
+++ b/biopet/seqstat.wdl
@@ -14,13 +14,13 @@ task Generate {
String library
String readgroup
- Int memory = 4
- Float memoryMultiplier = 2.5
+ String memory = "10G"
+ String javaXmx = "4G"
}
String toolCommand = if defined(toolJar)
- then "java -Xmx" + memory + "G -jar " + toolJar
- else "biopet-seqstat -Xmx" + memory + "G"
+ then "java -Xmx~{javaXmx} -jar " + toolJar
+ else "biopet-seqstat -Xmx~{javaXmx}"
command {
set -e -o pipefail
@@ -40,6 +40,6 @@ task Generate {
}
runtime {
- memory: ceil(memory * memoryMultiplier)
+ memory: memory
}
}
\ No newline at end of file
diff --git a/centrifuge.wdl b/centrifuge.wdl
index ac8cd5a..ec6652f 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -27,7 +27,7 @@ task Build {
Int? kmerCount
Int threads = 8
- Int memory = 20
+ String memory = "20G"
}
command {
@@ -81,7 +81,7 @@ task Classify {
Array[String]? excludeTaxIds
Int threads = 4
- Int memory = 8
+ String memory = "8G"
}
String outputFilePath = outputDir + "/centrifuge.out"
@@ -205,7 +205,7 @@ task Kreport {
Int? minLength
Int cores = 1
- Int memory = 4
+ String memory = "4G"
}
String kreportFilePath = outputDir + "/" + prefix + "." + suffix
diff --git a/collect-columns.wdl b/collect-columns.wdl
index 57d2467..fce0cfa 100644
--- a/collect-columns.wdl
+++ b/collect-columns.wdl
@@ -36,10 +36,10 @@ task CollectColumns {
File outputTable = outputPath
}
- Int memoryGigs = 4 + ceil(0.5 * length(inputTables))
+ Int memoryGb = 4 + ceil(0.5 * length(inputTables))
runtime {
- memory: "~{memoryGigs}G"
+ memory: "~{memoryGb}G"
docker: dockerImage
}
}
\ No newline at end of file
diff --git a/flash.wdl b/flash.wdl
index 8170360..03a3646 100644
--- a/flash.wdl
+++ b/flash.wdl
@@ -13,7 +13,7 @@ task Flash {
Boolean compress = true
Int threads = 2
- Int memory = 2
+ String memory = "2G"
}
command {
diff --git a/stringtie.wdl b/stringtie.wdl
index d9b7cdc..dd267aa 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -55,7 +55,7 @@ task Merge {
Boolean keepMergedTranscriptsWithRetainedIntrons = false
String? label
- Int memory = 10
+ String memory = "10G"
String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0"
}
--
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