From 21643dbda1283da2c57d1fb0dce05a38a4dba8ff Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Tue, 24 Jul 2018 14:10:13 +0200
Subject: [PATCH] reduce task complexities
---
biopet.wdl | 158 ++++++++++++++++++++++++-----------------------------
bwa.wdl | 8 +--
2 files changed, 74 insertions(+), 92 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 3b550be..e9fee2b 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -10,15 +10,13 @@ task BaseCounter {
String outputDir
String prefix
- Float? memory
- Float? memoryMultiplier
+ Int memory = 4
+ Float memoryMultiplier = 3.0
}
- Int mem = ceil(select_first([memory, 4.0]))
-
String toolCommand = if defined(toolJar)
- then "java -Xmx" + mem + "G -jar " +toolJar
- else "biopet-basecounter -Xmx" + mem + "G"
+ then "java -Xmx" + memory + "G -jar " +toolJar
+ else "biopet-basecounter -Xmx" + memory + "G"
command {
set -e -o pipefail
@@ -69,7 +67,7 @@ task BaseCounter {
}
runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
+ memory: ceil(memory * memoryMultiplier)
}
}
@@ -79,48 +77,46 @@ task ExtractAdaptersFastqc {
String? preCommand
File inputFile
String outputDir
- String? adapterOutputFilePath = outputDir + "/adapter.list"
- String? contamsOutputFilePath = outputDir + "/contaminations.list"
+ String adapterOutputFilePath = outputDir + "/adapter.list"
+ String contamsOutputFilePath = outputDir + "/contaminations.list"
Boolean? skipContams
File? knownContamFile
File? knownAdapterFile
Float? adapterCutoff
Boolean? outputAsFasta
- Float? memory
- Float? memoryMultiplier
+ Int memory = 4
+ Float memoryMultiplier = 2.5
}
- Int mem = ceil(select_first([memory, 4.0]))
-
String toolCommand = if defined(toolJar)
- then "java -Xmx" + mem + "G -jar " +toolJar
- else "biopet-extractadaptersfastqc -Xmx" + mem + "G"
+ then "java -Xmx" + memory + "G -jar " +toolJar
+ else "biopet-extractadaptersfastqc -Xmx" + memory + "G"
command {
- set -e
- ~{preCommand}
- mkdir -p ~{outputDir}
- ~{toolCommand} \
- --inputFile ~{inputFile} \
- ~{"--adapterOutputFile " + adapterOutputFilePath } \
- ~{"--contamsOutputFile " + contamsOutputFilePath } \
- ~{"--knownContamFile " + knownContamFile} \
- ~{"--knownAdapterFile " + knownAdapterFile} \
- ~{"--adapterCutoff " + adapterCutoff} \
- ~{true="--skipContams" false="" skipContams} \
- ~{true="--outputAsFasta" false="" outputAsFasta}
+ set -e
+ ~{preCommand}
+ mkdir -p ~{outputDir}
+ ~{toolCommand} \
+ --inputFile ~{inputFile} \
+ ~{"--adapterOutputFile " + adapterOutputFilePath } \
+ ~{"--contamsOutputFile " + contamsOutputFilePath } \
+ ~{"--knownContamFile " + knownContamFile} \
+ ~{"--knownAdapterFile " + knownAdapterFile} \
+ ~{"--adapterCutoff " + adapterCutoff} \
+ ~{true="--skipContams" false="" skipContams} \
+ ~{true="--outputAsFasta" false="" outputAsFasta}
}
output {
- File adapterOutputFile = select_first([adapterOutputFilePath])
- File contamsOutputFile = select_first([contamsOutputFilePath])
- Array[String] adapterList = read_lines(select_first([adapterOutputFilePath]))
- Array[String] contamsList = read_lines(select_first([contamsOutputFilePath]))
+ File adapterOutputFile = adapterOutputFilePath
+ File contamsOutputFile = contamsOutputFilePath
+ Array[String] adapterList = read_lines(adapterOutputFilePath)
+ Array[String] contamsList = read_lines(contamsOutputFilePath)
}
runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 2.5]))
+ memory: ceil(memory * memoryMultiplier)
}
}
@@ -128,18 +124,16 @@ task FastqSplitter {
input {
String? preCommand
File inputFastq
- Array[String] outputPaths
+ Array[String]+ outputPaths
File? toolJar
- Float? memory
- Float? memoryMultiplier
+ Int memory = 4
+ Float memoryMultiplier = 2.5
}
- Int mem = ceil(select_first([memory, 4.0]))
-
String toolCommand = if defined(toolJar)
- then "java -Xmx" + mem + "G -jar " +toolJar
- else "biopet-fastqsplitter -Xmx" + mem + "G"
+ then "java -Xmx" + memory + "G -jar " +toolJar
+ else "biopet-fastqsplitter -Xmx" + memory + "G"
command {
set -e -o pipefail
@@ -159,7 +153,7 @@ task FastqSplitter {
}
runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 2.5]))
+ memory: ceil(memory * memoryMultiplier, 2.5)
}
}
@@ -174,15 +168,13 @@ task FastqSync {
String out2path
File? toolJar
- Float? memory
- Float? memoryMultiplier
+ Int memory = 4
+ Float memoryMultiplier = 2.5
}
- Int mem = ceil(select_first([memory, 4.0]))
-
String toolCommand = if defined(toolJar)
- then "java -Xmx" + mem + "G -jar " +toolJar
- else "biopet-fastqsync -Xmx" + mem + "G"
+ then "java -Xmx" + memory + "G -jar " +toolJar
+ else "biopet-fastqsync -Xmx" + memory + "G"
command {
set -e -o pipefail
@@ -203,7 +195,7 @@ task FastqSync {
}
runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 2.5]))
+ memory: ceil(memory * memoryMultiplier)
}
}
@@ -219,15 +211,13 @@ task SampleConfig {
String? jsonOutputPath
String? tsvOutputPath
- Float? memory
- Float? memoryMultiplier
+ Int memory = 4
+ Float memoryMultiplier = 2.0
}
- Int mem = ceil(select_first([memory, 4.0]))
-
String toolCommand = if defined(toolJar)
- then "java -Xmx" + mem + "G -jar " +toolJar
- else "biopet-sampleconfig -Xmx" + mem + "G"
+ then "java -Xmx" + memory + "G -jar " +toolJar
+ else "biopet-sampleconfig -Xmx" + memory + "G"
command {
set -e -o pipefail
@@ -250,7 +240,7 @@ task SampleConfig {
}
runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
+ memory: ceil(memory * memoryMultiplier)
}
}
@@ -264,14 +254,13 @@ task ScatterRegions {
Int? scatterSize
File? regions
- Float? memory
- Float? memoryMultiplier
+ Int memory = 4
+ Float memoryMultiplier = 3.0
}
- Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(toolJar)
- then "java -Xmx" + mem + "G -jar " +toolJar
- else "biopet-scatterregions -Xmx" + mem + "G"
+ then "java -Xmx" + memory + "G -jar " +toolJar
+ else "biopet-scatterregions -Xmx" + memory + "G"
command {
set -e -o pipefail
@@ -289,7 +278,7 @@ task ScatterRegions {
}
runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
+ memory: ceil(memory * memoryMultiplier)
}
}
@@ -299,15 +288,14 @@ task Seqstat {
File? toolJar
File fastq
String outputFile
- Float? memory
- Float? memoryMultiplier
- }
- Int mem = ceil(select_first([memory, 4.0]))
+ Int memory = 4
+ Float memoryMultiplier = 2.0
+ }
String toolCommand = if defined(toolJar)
- then "java -Xmx" + mem + "G -jar " + toolJar
- else "biopet-seqstat -Xmx" + mem + "G"
+ then "java -Xmx" + memory + "G -jar " + toolJar
+ else "biopet-seqstat -Xmx" + memory + "G"
command {
set -e -o pipefail
@@ -323,7 +311,7 @@ task Seqstat {
}
runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
+ memory: ceil(memory * memoryMultiplier)
}
}
@@ -337,15 +325,13 @@ task ValidateAnnotation {
File refFastaIndex
File refDict
- Float? memory
- Float? memoryMultiplier
+ Int memory = 4
+ Float memoryMultiplier = 2.0
}
- Int mem = ceil(select_first([memory, 4.0]))
-
String toolCommand = if defined(toolJar)
- then "java -Xmx" + mem + "G -jar " + toolJar
- else "biopet-validateannotation -Xmx" + mem + "G"
+ then "java -Xmx" + memory + "G -jar " + toolJar
+ else "biopet-validateannotation -Xmx" + memory + "G"
command {
set -e -o pipefail
@@ -361,7 +347,7 @@ task ValidateAnnotation {
}
runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
+ memory: ceil(memory * memoryMultiplier)
}
}
@@ -372,15 +358,13 @@ task ValidateFastq {
File fastq1
File? fastq2
- Float? memory
- Float? memoryMultiplier
+ Int memory = 4
+ Float memoryMultiplier = 2.0
}
- Int mem = ceil(select_first([memory, 4.0]))
-
String toolCommand = if defined(toolJar)
- then "java -Xmx" + mem + "G -jar " + toolJar
- else "biopet-validatefastq -Xmx" + mem + "G"
+ then "java -Xmx" + memory + "G -jar " + toolJar
+ else "biopet-validatefastq -Xmx" + memory + "G"
command {
set -e -o pipefail
@@ -395,7 +379,7 @@ task ValidateFastq {
}
runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
+ memory: ceil(memory * memoryMultiplier)
}
}
@@ -409,15 +393,13 @@ task ValidateVcf {
File refFastaIndex
File refDict
- Float? memory
- Float? memoryMultiplier
+ Int memory = 4
+ Float memoryMultiplier = 2.0
}
- Int mem = ceil(select_first([memory, 4.0]))
-
String toolCommand = if defined(toolJar)
- then "java -Xmx" + mem + "G -jar " + toolJar
- else "biopet-validatevcf -Xmx" + mem + "G"
+ then "java -Xmx" + memory + "G -jar " + toolJar
+ else "biopet-validatevcf -Xmx" + memory + "G"
command {
set -e -o pipefail
@@ -432,6 +414,6 @@ task ValidateVcf {
}
runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 2.0]))
+ memory: ceil(memory * memoryMultiplier)
}
}
diff --git a/bwa.wdl b/bwa.wdl
index d012b38..fb3ab9b 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -10,8 +10,8 @@ task mem {
String outputPath
String? readgroup
- Int? threads
- Int? memory
+ Int threads = 1
+ Int memory = 8
}
command {
@@ -28,8 +28,8 @@ task mem {
}
runtime{
- cpu: select_first([threads,1])
- memory: select_first([memory,8])
+ cpu: threads
+ memory: memory
}
}
--
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