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Commit 21643dbd authored by Cats's avatar Cats
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reduce task complexities

parent 70216915
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1 merge request!36Make optional values mandatory where appropriate
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biopet.wdl
+ 70
− 88
View file @ 21643dbd
......@@ -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)
}
}
bwa.wdl
+ 4
− 4
View file @ 21643dbd
......@@ -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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