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Unverified Commit 99dbe5f3 authored by Ruben Vorderman's avatar Ruben Vorderman Committed by GitHub
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Merge pull request #24 from biowdl/BIOWDL-36 

Changes after testing
parents e5b86e77 9305e435
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centrifuge.wdl
+ 3
− 3
View file @ 99dbe5f3
......@@ -86,7 +86,7 @@ task Classify {
mkdir -p ${outputDir}
${preCommand}
centrifuge \
${"-p " + threads} \
${"-p " + select_first([threads, 4])} \
${"-x " + indexPrefix} \
${true="-f" false="" fastaInput} \
${true="-k" false="" defined(assignments)} ${assignments} \
......@@ -108,8 +108,8 @@ task Classify {
}
runtime {
cpu: select_first([threads, 1])
memory: select_first([memory, 4])
cpu: select_first([threads, 4])
memory: select_first([memory, 8])
}
}
......
gatk.wdl
+ 28
− 17
View file @ 99dbe5f3
......@@ -19,13 +19,12 @@ task ApplyBQSR {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G"
else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
${preCommand}
${toolCommand} \
-Xms${mem}G -jar ${gatkJar} \
ApplyBQSR \
--create-output-bam-md5 \
--add-output-sam-program-record \
......@@ -56,12 +55,23 @@ task BaseRecalibrator {
File inputBamIndex
String recalibrationReportPath
Array[File]+ sequenceGroupInterval
Array[File]+ knownIndelsSitesVCFs
Array[File]+ knownIndelsSitesIndices
Array[File]? knownIndelsSitesVCFs
Array[File]? knownIndelsSitesIndices
File? dbsnpVCF
File? dbsnpVCFindex
File refDict
File refFasta
File refFastaIndex
Array[File]+ knownIndelsSitesVCFsArg = flatten([
select_first([knownIndelsSitesVCFs, []]),
select_all([dbsnpVCF])
])
Array[File]+ knownIndelsSitesIndicesArg = flatten([
select_first([knownIndelsSitesIndices, []]),
select_all([dbsnpVCFindex])
])
Float? memory
Float? memoryMultiplier
......@@ -69,7 +79,7 @@ task BaseRecalibrator {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G"
else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
......@@ -80,7 +90,7 @@ task BaseRecalibrator {
-I ${inputBam} \
--use-original-qualities \
-O ${recalibrationReportPath} \
--known-sites ${sep=" --known-sites " knownIndelsSitesVCFs} \
--known-sites ${sep=" --known-sites " knownIndelsSitesVCFsArg} \
-L ${sep=" -L " sequenceGroupInterval}
}
......@@ -115,7 +125,7 @@ task CombineGVCFs {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G"
else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
......@@ -123,7 +133,6 @@ task CombineGVCFs {
if [ ${length(gvcfFiles)} -gt 1 ]; then
${toolCommand} \
-Xmx${mem}G -jar ${gatkJar} \
CombineGVCFs \
-R ${refFasta} \
-O ${outputPath} \
......@@ -159,7 +168,7 @@ task GatherBqsrReports {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G"
else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
......@@ -193,8 +202,8 @@ task GenotypeGVCFs {
File refFastaIndex
File refDict
File dbsnpVCF
File dbsnpVCFindex
File? dbsnpVCF
File? dbsnpVCFindex
Int? compressionLevel
Float? memory
......@@ -204,18 +213,17 @@ task GenotypeGVCFs {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G"
else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
${preCommand}
${toolCommand} \
-Xmx${mem}G -jar ${gatkJar} \
GenotypeGVCFs \
-R ${refFasta} \
-O ${outputPath} \
-D ${dbsnpVCF} \
${"-D " + dbsnpVCF} \
-G StandardAnnotation \
--only-output-calls-starting-in-intervals \
-new-qual \
......@@ -247,24 +255,27 @@ task HaplotypeCallerGvcf {
Int? compressionLevel
String? gatkJar
File? dbsnpVCF
File? dbsnpVCFindex
Float? memory
Float? memoryMultiplier
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G"
else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
${preCommand}
${toolCommand} \
-Xmx${mem}G -jar ${gatkJar} \
HaplotypeCaller \
-R ${refFasta} \
-O ${gvcfPath} \
-I ${sep=" -I " inputBams} \
-L ${sep=' -L ' intervalList} \
${"-D " + dbsnpVCF} \
-contamination ${default=0 contamination} \
-ERC GVCF
}
......@@ -297,7 +308,7 @@ task SplitNCigarReads {
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk -Xmx" + mem + "G"
else "gatk --java-options -Xmx" + mem + "G"
command {
set -e -o pipefail
......
picard.wdl
+ 5
− 5
View file @ 99dbe5f3
......@@ -11,7 +11,7 @@ task ScatterIntervalList {
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "gatk -Xmx" + mem + "G"
else "picard -Xmx" + mem + "G"
command {
set -e -o pipefail
......@@ -52,7 +52,7 @@ task GatherBamFiles {
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "gatk -Xmx" + mem + "G"
else "picard -Xmx" + mem + "G"
command {
set -e -o pipefail
......@@ -100,7 +100,7 @@ task MarkDuplicates {
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "gatk -Xmx" + mem + "G"
else "picard -Xmx" + mem + "G"
command {
set -e -o pipefail
......@@ -148,7 +148,7 @@ task MergeVCFs {
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "gatk -Xmx" + mem + "G"
else "picard -Xmx" + mem + "G"
command {
set -e -o pipefail
......@@ -182,7 +182,7 @@ task SamToFastq {
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "gatk -Xmx" + mem + "G"
else "picard -Xmx" + mem + "G"
command {
set -e -o pipefail
......
star.wdl
+ 1
− 1
View file @ 99dbe5f3
......@@ -2,7 +2,7 @@ task Star {
String? preCommand
Array[File] inputR1
Array[File?] inputR2
Array[File]? inputR2
String genomeDir
String outFileNamePrefix
......
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