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Commit 1a455271 authored by Cats's avatar Cats
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memory Int -> String part 2

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common.wdl
+ 4
− 4
View file @ 1a455271
......@@ -16,7 +16,7 @@ task AppendToStringArray {
}
runtime {
memory: 1
memory: "1G"
}
}
......@@ -66,7 +66,7 @@ task ConcatenateTextFiles {
}
runtime {
memory: 1
memory: "1G"
}
}
......@@ -129,7 +129,7 @@ task MapMd5 {
}
runtime {
memory: 1
memory: "1G"
docker: dockerImage
}
}
......@@ -193,7 +193,7 @@ task StringArrayMd5 {
}
runtime {
memory: 1
memory: "1G"
docker: dockerImage
}
}
......
cutadapt.wdl
+ 1
− 1
View file @ 1a455271
......@@ -61,7 +61,7 @@ task Cutadapt {
#~{"--compression-level=" + compressionLevel} \
Boolean Z = true # equal to compressionLevel=1 # Fixme: replace once upstream is fixed.
Int cores = 1
Int memory = 4
String memory = "4G"
String dockerImage = "quay.io/biocontainers/cutadapt:2.4--py37h14c3975_0"
}
......
fastqc.wdl
+ 3
− 3
View file @ 1a455271
......@@ -67,7 +67,7 @@ task Fastqc {
task GetConfiguration {
input {
String dockerTag = "0.11.7--4"
String dockerImage = "quay.io/biocontainers/fastqc:0.11.7--4"
}
command <<<
......@@ -86,7 +86,7 @@ task GetConfiguration {
}
runtime {
memory: 2 # Needs more than 1 to pull the docker image
docker: "quay.io/biocontainers/fastqc:" + dockerTag
memory: "2G" # Needs more than 1 to pull the docker image
docker: dockerImage
}
}
fastqsplitter.wdl
+ 1
− 1
View file @ 1a455271
......@@ -58,7 +58,7 @@ task Fastqsplitter {
Int memory = if fastqsplitterMemory <= 2 then 2 else fastqsplitterMemory
runtime {
memory: memory
memory: "~{memory}G"
docker: dockerImage
cpu: cores
}
......
gatk.wdl
+ 58
− 56
View file @ 1a455271
......@@ -12,15 +12,15 @@ task ApplyBQSR {
File referenceFastaDict
File referenceFastaFai
Int memory = 4
Float memoryMultiplier = 3.0
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p $(dirname ~{outputBamPath})
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx} \
ApplyBQSR \
--create-output-bam-md5 \
--add-output-sam-program-record \
......@@ -43,7 +43,7 @@ task ApplyBQSR {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -62,15 +62,15 @@ task BaseRecalibrator {
File referenceFastaDict
File referenceFastaFai
Int memory = 4
Float memoryMultiplier = 3.0
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p $(dirname ~{recalibrationReportPath})
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx} \
BaseRecalibrator \
-R ~{referenceFasta} \
-I ~{inputBam} \
......@@ -87,7 +87,7 @@ task BaseRecalibrator {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -101,15 +101,15 @@ task CombineGVCFs {
File referenceFastaDict
File referenceFastaFai
Int memory = 4
Float memoryMultiplier = 3.0
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p $(dirname ~{outputPath})
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx}G \
CombineGVCFs \
-R ~{referenceFasta} \
-O ~{outputPath} \
......@@ -124,7 +124,7 @@ task CombineGVCFs {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -134,15 +134,15 @@ task GatherBqsrReports {
Array[File] inputBQSRreports
String outputReportPath
Int memory = 4
Float memoryMultiplier = 3.0
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p $(dirname ~{outputReportPath})
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx} \
GatherBQSRReports \
-I ~{sep=' -I ' inputBQSRreports} \
-O ~{outputReportPath}
......@@ -154,7 +154,7 @@ task GatherBqsrReports {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -169,15 +169,16 @@ task GenotypeGVCFs {
File referenceFastaFai
File? dbsnpVCF
File? dbsnpVCFIndex
Int memory = 6
Float memoryMultiplier = 3.0
String memory = "18G"
String javaXmx = "6G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p $(dirname ~{outputPath})
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx} \
GenotypeGVCFs \
-R ~{referenceFasta} \
-O ~{outputPath} \
......@@ -197,7 +198,7 @@ task GenotypeGVCFs {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -214,15 +215,16 @@ task HaplotypeCallerGvcf {
Float contamination = 0.0
File? dbsnpVCF
File? dbsnpVCFIndex
Int memory = 4
Float memoryMultiplier = 3
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p $(dirname ~{gvcfPath})
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx} \
HaplotypeCaller \
-R ~{referenceFasta} \
-O ~{gvcfPath} \
......@@ -240,7 +242,7 @@ task HaplotypeCallerGvcf {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -262,15 +264,15 @@ task MuTect2 {
Array[File]+ intervals
String outputStats = outputVcf + ".stats"
Int memory = 4
Float memoryMultiplier = 4
String memory = "16G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
mkdir -p $(dirname ~{outputVcf})
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx} \
Mutect2 \
-R ~{referenceFasta} \
-I ~{sep=" -I " inputBams} \
......@@ -292,7 +294,7 @@ task MuTect2 {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -300,14 +302,14 @@ task LearnReadOrientationModel {
input {
Array[File]+ f1r2TarGz
Int memory = 12
Float memoryMultiplier = 2
String memory = "24G"
String javaXmx = "12G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx} \
LearnReadOrientationModel \
-I ~{sep=" -I " f1r2TarGz} \
-O "artifact-priors.tar.gz"
......@@ -319,7 +321,7 @@ task LearnReadOrientationModel {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -327,14 +329,14 @@ task MergeStats {
input {
Array[File]+ stats
Int memory = 14
Float memoryMultiplier = 2
String memory = "28G"
String javaXmx = "14G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx} \
MergeMutectStats \
-stats ~{sep=" -stats " stats} \
-O "merged.stats"
......@@ -346,7 +348,7 @@ task MergeStats {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -360,14 +362,14 @@ task GetPileupSummaries {
File sitesForContaminationIndex
String outputPrefix
Int memory = 12
Float memoryMultiplier = 2
String memory = "24G"
String javaXmx = "12G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx} \
GetPileupSummaries \
-I ~{sampleBam} \
-V ~{variantsForContamination} \
......@@ -381,7 +383,7 @@ task GetPileupSummaries {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -390,14 +392,14 @@ task CalculateContamination {
File tumorPileups
File? normalPileups
Int memory = 12
Float memoryMultiplier = 2
String memory = "24G"
String javaXmx = "12G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx} \
CalculateContamination \
-I ~{tumorPileups} \
~{"-matched " + normalPileups} \
......@@ -412,7 +414,7 @@ task CalculateContamination {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -431,15 +433,15 @@ task FilterMutectCalls {
File mutect2Stats
String? extraArgs
Int memory = 12
Float memoryMultiplier = 2
String memory = "24G"
String javaXmx = "12G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.2.0--1"
}
command {
set -e
mkdir -p $(dirname ~{outputVcf})
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx} \
FilterMutectCalls \
-R ~{referenceFasta} \
-V ~{unfilteredVcf} \
......@@ -462,7 +464,7 @@ task FilterMutectCalls {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -476,15 +478,15 @@ task SplitNCigarReads {
String outputBam
Array[File] intervals = []
Int memory = 4
Float memoryMultiplier = 4
String memory = "16G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
}
command {
set -e
mkdir -p $(dirname ~{outputBam})
gatk --java-options -Xmx~{memory}G \
gatk --java-options -Xmx~{javaXmx} \
SplitNCigarReads \
-I ~{inputBam} \
-R ~{referenceFasta} \
......@@ -499,7 +501,7 @@ task SplitNCigarReads {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -517,8 +519,8 @@ task CombineVariants {
Array[File]+ variantIndexes
String outputPath
Int memory = 12
Float memoryMultiplier = 2
String memory = "24G"
String javaXmx = "12G"
String dockerImage = "broadinstitute/gatk3:3.8-1"
}
......@@ -538,7 +540,7 @@ task CombineVariants {
printf -- "-V:%s %s " "${ids[i]}" "${vars[i]}"
done
)
java -Xmx~{memory}G -jar ~{installDir}/GenomeAnalysisTK.jar \
java -Xmx~{javaXmx} -jar ~{installDir}/GenomeAnalysisTK.jar \
-T CombineVariants \
-R ~{referenceFasta} \
--genotypemergeoption ~{genotypeMergeOption} \
......@@ -555,6 +557,6 @@ task CombineVariants {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
hisat2.wdl
+ 2
− 2
View file @ 1a455271
......@@ -13,7 +13,7 @@ task Hisat2 {
Boolean downstreamTranscriptomeAssembly = true
Int threads = 1
Int memory = 48
String memory = "48G"
# quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1
# is a combination of hisat2 and samtools
# hisat2=2.1.0, samtools=1.8
......@@ -41,7 +41,7 @@ task Hisat2 {
}
runtime {
memory: (memory / threads) + 1
memory: memory
cpu: threads + 1
docker: dockerImage
}
......
htseq.wdl
+ 1
− 1
View file @ 1a455271
......@@ -12,7 +12,7 @@ task HTSeqCount {
String? idattr
Array[String] additionalAttributes = []
Int memory = 40
String memory = "40G"
String dockerImage = "quay.io/biocontainers/htseq:0.9.1--py36h7eb728f_2"
}
......
macs2.wdl
+ 3
− 2
View file @ 1a455271
......@@ -11,7 +11,8 @@ task PeakCalling {
Boolean nomodel = false
Int threads = 1
Int memory = 8
String memory = "8G"
String dockerImage = "quay.io/biocontainers/macs2:2.1.2--py27r351_0"
}
command {
......@@ -31,6 +32,6 @@ task PeakCalling {
runtime {
cpu: threads
memory: memory
docker: "quay.io/biocontainers/macs2:2.1.2--py27r351_0"
docker: dockerImage
}
}
\ No newline at end of file
manta.wdl
+ 3
− 3
View file @ 1a455271
......@@ -16,7 +16,7 @@ task Somatic {
Boolean exome = false
Int cores = 1
Int memory = 4
Int memoryGb = 4
String dockerImage = "quay.io/biocontainers/manta:1.4.0--py27_1"
}
......@@ -33,7 +33,7 @@ task Somatic {
~{runDir}/runWorkflow.py \
-m local \
-j ~{cores} \
-g ~{memory}
-g ~{memoryGb}
}
output {
......@@ -53,7 +53,7 @@ task Somatic {
runtime {
cpu: cores
memory: memory
memory: "~{memoryGb}G"
docker: dockerImage
}
}
minimap2.wdl
+ 2
− 2
View file @ 1a455271
......@@ -31,7 +31,7 @@ task Indexing {
Int? splitIndex
Int cores = 1
Int memory = 4
String memory = "4G"
String dockerImage = "quay.io/biocontainers/minimap2:2.17--h84994c4_0"
}
......@@ -90,7 +90,7 @@ task Mapping {
Boolean? addMDtagToSAM
Int cores = 4
Int memory = 7
String memory = "30G"
String dockerImage = "quay.io/biocontainers/minimap2:2.17--h84994c4_0"
}
......
multiqc.wdl
+ 1
− 1
View file @ 1a455271
......@@ -38,7 +38,7 @@ task MultiQC {
Boolean quiet = false
Array[Boolean] finished = [] # An array of booleans that can be used to let multiqc wait on stuff.
Int memory = 4
String memory = "4G"
String dockerImage = "quay.io/biocontainers/multiqc:1.7--py_1"
}
......
picard.wdl
+ 44
− 44
View file @ 1a455271
......@@ -6,15 +6,15 @@ task BedToIntervalList {
File dict
String outputPath
Int memory = 4
Float memoryMultiplier = 3.0
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
set -e
mkdir -p $(dirname "~{outputPath}")
picard -Xmx~{memory}G \
picard -Xmx~{javaXmx} \
BedToIntervalList \
I=~{bedFile} \
O=~{outputPath} \
......@@ -27,7 +27,7 @@ task BedToIntervalList {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -50,8 +50,8 @@ task CollectMultipleMetrics {
Boolean collectSequencingArtifactMetrics = true
Boolean collectQualityYieldMetrics = true
Int memory = 8
Float memoryMultiplier = 4
String memory = "32G"
String javaXmx = "8G"
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
......@@ -59,7 +59,7 @@ task CollectMultipleMetrics {
command {
set -e
mkdir -p $(dirname "~{basename}")
picard -Xmx~{memory}G \
picard -Xmx~{javaXmx} \
CollectMultipleMetrics \
I=~{inputBam} \
R=~{referenceFasta} \
......@@ -121,7 +121,7 @@ task CollectMultipleMetrics {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -133,15 +133,15 @@ task CollectRnaSeqMetrics {
String basename
String strandSpecificity = "NONE"
Int memory = 8
Float memoryMultiplier = 4.0
String memory = "32G"
String javaXmx = "8G"
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
set -e
mkdir -p $(dirname "~{basename}")
picard -Xmx~{memory}G \
picard -Xmx~{javaXmx} \
CollectRnaSeqMetrics \
I=~{inputBam} \
O=~{basename}.RNA_Metrics \
......@@ -157,7 +157,7 @@ task CollectRnaSeqMetrics {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -172,15 +172,15 @@ task CollectTargetedPcrMetrics {
Array[File]+ targetIntervals
String basename
Int memory = 4
Float memoryMultiplier = 3.0
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
set -e
mkdir -p $(dirname "~{basename}")
picard -Xmx~{memory}G \
picard -Xmx~{javaXmx} \
CollectTargetedPcrMetrics \
I=~{inputBam} \
R=~{referenceFasta} \
......@@ -199,7 +199,7 @@ task CollectTargetedPcrMetrics {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -210,15 +210,15 @@ task GatherBamFiles {
Array[File]+ inputBamsIndex
String outputBamPath
Int memory = 4
Float memoryMultiplier = 3.0
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
set -e
mkdir -p $(dirname ~{outputBamPath})
picard -Xmx~{memory}G \
picard -Xmx~{javaXmx} \
GatherBamFiles \
INPUT=~{sep=' INPUT=' inputBams} \
OUTPUT=~{outputBamPath} \
......@@ -234,7 +234,7 @@ task GatherBamFiles {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -244,15 +244,15 @@ task GatherVcfs {
Array[File]+ inputVcfIndexes
String outputVcfPath = "out.vcf.gz"
Int memory = 4
Float memoryMultiplier = 3.0
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
set -e
mkdir -p $(dirname ~{outputVcfPath})
picard -Xmx~{memory}G \
picard -Xmx~{javaXmx} \
GatherVcfs \
INPUT=~{sep=' INPUT=' inputVcfs} \
OUTPUT=~{outputVcfPath}
......@@ -264,7 +264,7 @@ task GatherVcfs {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -276,8 +276,8 @@ task MarkDuplicates {
String outputBamPath
String metricsPath
Int memory = 8
Float memoryMultiplier = 3.0
String memory = "24G"
String javaXmx = "8G"
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
# The program default for READ_NAME_REGEX is appropriate in nearly every case.
......@@ -295,7 +295,7 @@ task MarkDuplicates {
command {
set -e
mkdir -p $(dirname ~{outputBamPath})
picard -Xmx~{memory}G \
picard -Xmx~{javaXmx} \
MarkDuplicates \
INPUT=~{sep=' INPUT=' inputBams} \
OUTPUT=~{outputBamPath} \
......@@ -318,7 +318,7 @@ task MarkDuplicates {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -329,8 +329,8 @@ task MergeVCFs {
Array[File]+ inputVCFsIndexes
String outputVcfPath
Int memory = 8
Float memoryMultiplier = 3.0
String memory = "24G"
String javaXmx = "8G"
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
......@@ -340,7 +340,7 @@ task MergeVCFs {
command {
set -e
mkdir -p $(dirname ~{outputVcfPath})
picard -Xmx~{memory}G \
picard -Xmx~{javaXmx} \
MergeVcfs \
INPUT=~{sep=' INPUT=' inputVCFs} \
OUTPUT=~{outputVcfPath}
......@@ -353,7 +353,7 @@ task MergeVCFs {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -363,8 +363,8 @@ task SamToFastq {
File inputBamIndex
Boolean paired = true
Int memory = 16 # High memory default to avoid crashes.
Float memoryMultiplier = 3.0
String memory = "48G"
String javaXmx = "16G" # High memory default to avoid crashes.
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
File? NONE
}
......@@ -375,7 +375,7 @@ task SamToFastq {
command {
set -e
picard -Xmx~{memory}G \
picard -Xmx~{javaXmx} \
SamToFastq \
I=~{inputBam} \
~{"FASTQ=" + outputRead1} \
......@@ -391,7 +391,7 @@ task SamToFastq {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -400,15 +400,15 @@ task ScatterIntervalList {
File interval_list
Int scatter_count
Int memory = 4
Float memoryMultiplier = 3.0
String memory = "12G"
String javaXmx = "4G"
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
command {
set -e
mkdir scatter_list
picard -Xmx~{memory}G \
picard -Xmx~{javaXmx} \
IntervalListTools \
SCATTER_COUNT=~{scatter_count} \
SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW \
......@@ -425,7 +425,7 @@ task ScatterIntervalList {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
......@@ -435,8 +435,8 @@ task SortVcf {
String outputVcfPath
File? dict
Int memory = 8
Float memoryMultiplier = 3.0
String memory = "24G"
String javaXmx = "8G"
String dockerImage = "quay.io/biocontainers/picard:2.20.5--0"
}
......@@ -444,7 +444,7 @@ task SortVcf {
command {
set -e
mkdir -p $(dirname ~{outputVcfPath})
picard -Xmx~{memory}G \
picard -Xmx~{javaXmx} \
SortVcf \
I=~{sep=" I=" vcfFiles} \
~{"SEQUENCE_DICTIONARY=" + dict} \
......@@ -458,6 +458,6 @@ task SortVcf {
runtime {
docker: dockerImage
memory: ceil(memory * memoryMultiplier)
memory: memory
}
}
\ No newline at end of file
samtools.wdl
+ 2
− 2
View file @ 1a455271
......@@ -171,7 +171,7 @@ task Fastq {
Int? compressionLevel
Int threads = 1
Int memory = 1
String memory = "1G"
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
......@@ -253,7 +253,7 @@ task View {
Int? MAPQthreshold
Int threads = 1
Int memory = 1
String memory = "1G"
String dockerImage = "quay.io/biocontainers/samtools:1.8--h46bd0b3_5"
}
String outputIndexPath = basename(outputFileName) + ".bai"
......
spades.wdl
+ 3
− 6
View file @ 1a455271
......@@ -25,16 +25,13 @@ task Spades {
Boolean? disableRepeatResolution
File? dataset
Int threads = 1
Float memoryGb = 16.0
Int memoryGb = 16
File? tmpDir
String? k
Float? covCutoff
Int? phredOffset
}
Int clusterMemory = ceil(memoryGb / threads * 1.2)
Int memoryArg = ceil(memoryGb)
command {
set -e -o pipefail
~{preCommand}
......@@ -61,7 +58,7 @@ task Spades {
~{true="--disable-rr" false="" disableRepeatResolution} \
~{"--dataset " + dataset} \
~{"--threads " + threads} \
~{"--memory " + memoryArg} \
~{"--memory " + memoryGb} \
~{"-k " + k} \
~{"--cov-cutoff " + covCutoff} \
~{"--phred-offset " + phredOffset}
......@@ -81,6 +78,6 @@ task Spades {
runtime {
cpu: threads
memory: clusterMemory
memory: "~{memoryGb}G"
}
}
\ No newline at end of file
star.wdl
+ 2
− 4
View file @ 1a455271
......@@ -15,7 +15,7 @@ task Star {
Int? limitBAMsortRAM
Int runThreadN = 4
Int memory = 48
String memory = "48G"
String dockerImage = "quay.io/biocontainers/star:2.6.0c--0"
}
......@@ -45,9 +45,7 @@ task Star {
runtime {
cpu: runThreadN
# Return memory per CPU here due to SGE backend.
# Can also work with slurms mem-per-cpu flag
memory: (memory / runThreadN) + 1
memory: memory
docker: dockerImage
}
}
......
strelka.wdl
+ 6
− 6
View file @ 1a455271
......@@ -15,7 +15,7 @@ task Germline {
Boolean rna = false
Int cores = 1
Int memory = 4
Int memoryGb = 4
String dockerImage = "quay.io/biocontainers/strelka:2.9.7--0"
}
......@@ -31,7 +31,7 @@ task Germline {
~{runDir}/runWorkflow.py \
-m local \
-j ~{cores} \
-g ~{memory}
-g ~{memoryGb}
}
output {
......@@ -42,7 +42,7 @@ task Germline {
runtime {
docker: dockerImage
cpu: cores
memory: memory
memory: "~{memoryGb}G"
}
}
......@@ -62,7 +62,7 @@ task Somatic {
Boolean exome = false
Int cores = 1
Int memory = 4
Int memoryGb = 4
String dockerImage = "quay.io/biocontainers/strelka:2.9.7--0"
File? doNotDefineThis #FIXME
......@@ -81,7 +81,7 @@ task Somatic {
~{runDir}/runWorkflow.py \
-m local \
-j ~{cores} \
-g ~{memory}
-g ~{memoryGb}
}
output {
......@@ -94,6 +94,6 @@ task Somatic {
runtime {
docker: dockerImage
cpu: cores
memory: memory
memory: "~{memoryGb}G"
}
}
\ No newline at end of file
stringtie.wdl
+ 1
− 1
View file @ 1a455271
......@@ -12,7 +12,7 @@ task Stringtie {
String? geneAbundanceFile
Int threads = 1
Int memory = 10
String memory = "10G"
String dockerImage = "quay.io/biocontainers/stringtie:1.3.4--py35_0"
}
......
talon.wdl
+ 7
− 7
View file @ 1a455271
......@@ -31,7 +31,7 @@ task CreateAbundanceFileFromDatabase {
File? filterPairingsFile
Int cores = 1
Int memory = 4
String memory = "4G"
String dockerImage = "biocontainers/talon:v4.2_cv2"
}
......@@ -80,7 +80,7 @@ task CreateGtfAbundanceFromDatabase {
File? filterPairingsFile
Int cores = 1
Int memory = 4
String memory = "4G"
String dockerImage = "biocontainers/talon:v4.2_cv2"
}
......@@ -132,7 +132,7 @@ task CreateGtfFromDatabase {
File? datasetFile
Int cores = 1
Int memory = 4
String memory = "4G"
String dockerImage = "biocontainers/talon:v4.2_cv2"
}
......@@ -184,7 +184,7 @@ task InitializeTalonDatabase {
Int cutoff3p = 300
Int cores = 1
Int memory = 10
String memory = "10G"
String dockerImage = "biocontainers/talon:v4.2_cv2"
}
......@@ -233,7 +233,7 @@ task MapAntisenseGenesToSense {
String annotationVersion
Int cores = 1
Int memory = 4
String memory = "4G"
String dockerImage = "biocontainers/talon:v4.2_cv2"
}
......@@ -273,7 +273,7 @@ task SummarizeDatasets {
File? datasetGroupsCSV
Int cores = 1
Int memory = 4
String memory = "4G"
String dockerImage = "biocontainers/talon:v4.2_cv2"
}
......@@ -318,7 +318,7 @@ task Talon {
Int minimumIdentity = 0
Int cores = 1
Int memory = 20
String memory = "20G"
String dockerImage = "biocontainers/talon:v4.2_cv2"
}
......
transcriptclean.wdl
+ 5
− 5
View file @ 1a455271
......@@ -30,7 +30,7 @@ task CleanSpliceJunctions {
File? variantFile
Int cores = 1
Int memory = 4
String memory = "4G"
String dockerImage = "biocontainers/transcriptclean:v1.0.8_cv1"
}
......@@ -72,7 +72,7 @@ task GetCorrectedSJsFromLog {
String outputPrefix
Int cores = 1
Int memory = 5
String memory = "5G"
String dockerImage = "biocontainers/transcriptclean:v1.0.8_cv1"
}
......@@ -110,7 +110,7 @@ task GetSJsFromGtf {
Int minIntronSize = 21
Int cores = 1
Int memory = 8
String memory = "8G"
String dockerImage = "biocontainers/transcriptclean:v1.0.8_cv1"
}
......@@ -150,7 +150,7 @@ task GetTranscriptCleanStats {
String outputPrefix
Int cores = 1
Int memory = 4
String memory = "4G"
String dockerImage = "biocontainers/transcriptclean:v1.0.8_cv1"
}
......@@ -197,7 +197,7 @@ task TranscriptClean {
Boolean? correctSJs
Int cores = 1
Int memory = 25
String memory = "25G"
String dockerImage = "biocontainers/transcriptclean:v1.0.8_cv1"
}
......
unicycler.wdl
+ 3
− 2
View file @ 1a455271
......@@ -12,8 +12,6 @@ task Unicycler {
Int? minFastaLength
Int? keep
Boolean? vcf
Int threads = 1
Int memory = 4
String? mode
Float? minBridgeQual
Int? linearSeqs
......@@ -45,6 +43,9 @@ task Unicycler {
File? contamination
String? scores
String? lowScore
Int threads = 1
String memory = "4G"
}
command {
......
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