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Unverified Commit 8fccf548 authored by Ruben Vorderman's avatar Ruben Vorderman Committed by GitHub
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Merge pull request #36 from biowdl/reduceComplexity 

Make optional values mandatory where appropriate
parents f3b6fa09 6425926f
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bioconda.wdl
+ 2
− 2
View file @ 8fccf548
......@@ -7,11 +7,11 @@ task installPrefix {
input {
Array[String] requirements
String prefix
String? condaPath
String condaPath = "conda"
}
command <<<
~{default="conda" condaPath} create \
~{condaPath} create \
--json -q \
--yes \
--override-channels \
......
biopet.wdl
+ 70
− 88
View file @ 8fccf548
......@@ -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)
}
}
......@@ -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
+ 10
− 7
View file @ 8fccf548
version 1.0
task mem {
task Mem {
input {
String? preCommand
File inputR1
......@@ -10,8 +10,8 @@ task mem {
String outputPath
String? readgroup
Int? threads
Int? memory
Int threads = 1
Int memory = 8
}
command {
......@@ -20,7 +20,10 @@ task mem {
~{preCommand}
bwa mem ~{"-t " + threads} \
~{"-R '" + readgroup + "'"} \
~{referenceFasta} ~{inputR1} ~{inputR2} | samtools sort --output-fmt BAM - > ~{outputPath}
~{referenceFasta} \
~{inputR1} \
~{inputR2} \
| samtools sort --output-fmt BAM - > ~{outputPath}
}
output {
......@@ -28,12 +31,12 @@ task mem {
}
runtime{
cpu: select_first([threads,1])
memory: select_first([memory,8])
cpu: threads
memory: memory
}
}
task index {
task Index {
input {
File fasta
String? preCommand
......
centrifuge.wdl
+ 32
− 30
View file @ 8fccf548
version 1.0
# Copyright Sequencing Analysis Support Core - Leiden University Medical Center 2018
#
# Tasks from centrifuge
......@@ -9,15 +10,15 @@ task Build {
File inputFasta
String centrifugeIndexBase
String? preCommand
String? centrifugeBuildExecutable = "centrifuge-build"
String centrifugeBuildExecutable = "centrifuge-build"
#Boolean? c = false
Boolean? largeIndex = false
Boolean? noAuto = false
Boolean largeIndex = false
Boolean noAuto = false
Int? bMax
Int? bMaxDivn
Boolean? noDiffCover = false
Boolean? noRef = false
Boolean? justRef = false
Boolean noDiffCover = false
Boolean noRef = false
Boolean justRef = false
Int? offRate
Int? fTabChars
File? nameTable
......@@ -25,8 +26,8 @@ task Build {
Int? seed
Int? kmerCount
Int? threads
Int? memory
Int threads = 8
Int memory = 20
}
command {
......@@ -55,15 +56,15 @@ task Build {
}
runtime {
cpu: select_first([threads, 8])
memory: select_first([memory, 20])
cpu: threads
memory: memory
}
}
task Classify {
input {
String outputDir
Boolean? compressOutput = true
Boolean compressOutput = true
String? preCommand
String indexPrefix
Array[File]? unpairedReads
......@@ -79,8 +80,8 @@ task Classify {
Array[String]? hostTaxIds
Array[String]? excludeTaxIds
Int? threads
Int? memory
Int threads = 4
Int memory = 8
}
String outputFilePath = outputDir + "/centrifuge.out"
......@@ -94,7 +95,7 @@ task Classify {
mkdir -p ~{outputDir}
~{preCommand}
centrifuge \
~{"-p " + select_first([threads, 4])} \
~{"-p " + threads} \
~{"-x " + indexPrefix} \
~{true="-f" false="" fastaInput} \
~{true="-k" false="" defined(assignments)} ~{assignments} \
......@@ -116,8 +117,8 @@ task Classify {
}
runtime {
cpu: select_first([threads, 4])
memory: select_first([memory, 8])
cpu: threads
memory: memory
}
}
......@@ -125,18 +126,18 @@ task Download {
input {
String libraryPath
Array[String]? domain
String? executable = "centrifuge-download"
String executable = "centrifuge-download"
String? preCommand
String? seqTaxMapPath
String? database = "refseq"
String database = "refseq"
String? assemblyLevel
String? refseqCategory
Array[String]? taxIds
Boolean? filterUnplaced = false
Boolean? maskLowComplexRegions = false
Boolean? downloadRnaSeqs = false
Boolean? modifyHeader = false
Boolean? downloadGiMap = false
Boolean filterUnplaced = false
Boolean maskLowComplexRegions = false
Boolean downloadRnaSeqs = false
Boolean modifyHeader = false
Boolean downloadGiMap = false
}
# This will use centrifuge-download to download.
......@@ -159,6 +160,7 @@ task Download {
~{true='-g' false='' downloadGiMap} \
~{database} ~{">> " + seqTaxMapPath}
}
output {
File seqTaxMap = "~{seqTaxMapPath}"
File library = libraryPath
......@@ -169,7 +171,7 @@ task Download {
task DownloadTaxonomy {
input {
String centrifugeTaxonomyDir
String? executable = "centrifuge-download"
String executable = "centrifuge-download"
String? preCommand
}
command {
......@@ -192,8 +194,8 @@ task Kreport {
File centrifugeOut
Boolean inputIsCompressed
String outputDir
String? suffix = "kreport"
String? prefix = "centrifuge"
String suffix = "kreport"
String prefix = "centrifuge"
String indexPrefix
Boolean? onlyUnique
Boolean? showZeros
......@@ -201,8 +203,8 @@ task Kreport {
Int? minScore
Int? minLength
Int? cores
Int? memory
Int cores = 1
Int memory = 4
}
String kreportFilePath = outputDir + "/" + prefix + "." + suffix
......@@ -226,7 +228,7 @@ task Kreport {
}
runtime {
cpu: select_first([cores, 1])
memory: select_first([memory, 4])
cpu: cores
memory: memory
}
}
common.wdl
+ 2
− 2
View file @ 8fccf548
......@@ -38,8 +38,8 @@ task ConcatenateTextFiles {
input {
Array[File] fileList
String combinedFilePath
Boolean? unzip = false
Boolean? zip = false
Boolean unzip = false
Boolean zip = false
}
command {
......
cutadapt.wdl
+ 35
− 22
View file @ 8fccf548
version 1.0
task cutadapt {
task Cutadapt {
input {
File read1
File? read2
......@@ -8,8 +8,8 @@ task cutadapt {
String? read2output
String? format
String? preCommand
Int? cores = 1
Int? memory = 4
Int cores = 1
Int memory = 4
Array[String]+? adapter
Array[String]+? front
Array[String]+? anywhere
......@@ -69,16 +69,19 @@ task cutadapt {
~{preCommand}
cutadapt \
~{"--cores=" + cores} \
~{true="-a " false="" defined(adapter)} ~{sep=" -a " adapter} \
~{true="-A " false="" defined(adapterRead2)} ~{sep=" -A " adapterRead2} \
~{true="-g " false="" defined(front)} ~{sep=" -g " front} \
~{true="-G " false="" defined(frontRead2)} ~{sep=" -G " frontRead2} \
~{true="-b " false="" defined(anywhere)} ~{sep=" -b " anywhere} \
~{true="-B " false="" defined(anywhereRead2)} ~{sep=" -B " anywhereRead2} \
~{true="-a" false="" defined(adapter)} ~{sep=" -a " adapter} \
~{true="-A" false="" defined(adapterRead2)} ~{sep=" -A " adapterRead2} \
~{true="-g" false="" defined(front)} ~{sep=" -g " front} \
~{true="-G" false="" defined(frontRead2)} ~{sep=" -G " frontRead2} \
~{true="-b" false="" defined(anywhere)} ~{sep=" -b " anywhere} \
~{true="-B" false="" defined(anywhereRead2)} ~{sep=" -B " anywhereRead2} \
--output ~{read1output} ~{"--paired-output " + read2output} \
~{"--to-short-output " + tooShortOutputPath} ~{"--to-short-paired-output " + tooShortPairedOutputPath} \
~{"--to-long-output " + tooLongOutputPath} ~{"--to-long-paired-output " + tooLongPairedOutputPath} \
~{"--untrimmed-output " + untrimmedOutputPath} ~{"--untrimmed-paired-output " + untrimmedPairedOutputPath} \
~{"--to-short-output " + tooShortOutputPath} \
~{"--to-short-paired-output " + tooShortPairedOutputPath} \
~{"--to-long-output " + tooLongOutputPath} \
~{"--to-long-paired-output " + tooLongPairedOutputPath} \
~{"--untrimmed-output " + untrimmedOutputPath} \
~{"--untrimmed-paired-output " + untrimmedPairedOutputPath} \
~{"--pair-filter " + pairFilter} \
~{"--error-rate " + errorRate} \
~{"--times " + times} \
......@@ -99,14 +102,24 @@ task cutadapt {
~{"--info-file " + infoFilePath } \
~{"--rest-file " + restFilePath } \
~{"--wildcard-file " + wildcardFilePath} \
~{true="--match-read-wildcards" false="" matchReadWildcards} ~{true="--no-match-adapter-wildcards" false="" noMatchAdapterWildcards} \
~{true="--no-trim" false="" noTrim} ~{true="--mask-adapter" false="" maskAdapter} \
~{true="--no-indels" false="" noIndels} ~{true="--trim-n" false="" trimN} \
~{true="--interleaved" false="" interleaved} ~{true="--discard-trimmed" false="" discardTrimmed } \
~{true="--colorspace" false="" colorspace} ~{true="--double-encode" false="" doubleEncode} \
~{true="--strip-f3" false="" stripF3} ~{true="--maq" false="" maq} ~{true="--bwa" false="" bwa} \
~{true="--zero-cap" false="" zeroCap} ~{true="--no-zero-cap" false="" noZeroCap} \
~{read1} ~{read2} ~{"> " + reportPath}
~{true="--match-read-wildcards" false="" matchReadWildcards} \
~{true="--no-match-adapter-wildcards" false="" noMatchAdapterWildcards} \
~{true="--no-trim" false="" noTrim} \
~{true="--mask-adapter" false="" maskAdapter} \
~{true="--no-indels" false="" noIndels} \
~{true="--trim-n" false="" trimN} \
~{true="--interleaved" false="" interleaved} \
~{true="--discard-trimmed" false="" discardTrimmed } \
~{true="--colorspace" false="" colorspace} \
~{true="--double-encode" false="" doubleEncode} \
~{true="--strip-f3" false="" stripF3} \
~{true="--maq" false="" maq} \
~{true="--bwa" false="" bwa} \
~{true="--zero-cap" false="" zeroCap} \
~{true="--no-zero-cap" false="" noZeroCap} \
~{read1} \
~{read2} \
~{"> " + reportPath}
}
output{
......@@ -125,7 +138,7 @@ task cutadapt {
}
runtime {
cpu: select_first([cores])
memory: select_first([memory])
cpu: cores
memory: memory
}
}
fastqc.wdl
+ 6
− 6
View file @ 8fccf548
version 1.0
task fastqc {
task Fastqc {
input {
File seqFile
String outdirPath
......@@ -8,11 +8,11 @@ task fastqc {
Boolean? casava
Boolean? nano
Boolean? noFilter
Boolean? extract = true
Boolean extract = true
Boolean? nogroup
Int? minLength
String? format
Int? threads = 1
Int threads = 1
File? contaminants
File? adapters
File? limits
......@@ -56,14 +56,14 @@ task fastqc {
}
runtime {
cpu: select_first([threads])
cpu: threads
}
}
task getConfiguration {
task GetConfiguration {
input {
String? preCommand
String? fastqcDirFile = "fastqcDir.txt"
String fastqcDirFile = "fastqcDir.txt"
}
command {
......
flash.wdl
+ 8
− 8
View file @ 8fccf548
version 1.0
task flash {
task Flash {
input {
String? preCommand
File inputR1
File inputR2
String outdirPath
String? outPrefix = "flash"
String outPrefix = "flash"
Int? minOverlap
Int? maxOverlap
Boolean? compress = true
Int? threads
Int? memory
Boolean compress = true
Int threads = 2
Int memory = 2
}
command {
......@@ -22,7 +22,7 @@ task flash {
~{"--threads=" + threads} \
~{"--output-directory=" + outdirPath} \
~{"--output-prefix=" + outPrefix} \
~{true="--compress " false="" defined(compress)} \
~{true="--compress " false="" compress} \
~{"--min-overlap=" + minOverlap} \
~{"--max-overlap=" + maxOverlap} \
~{inputR1} ~{inputR2}
......@@ -37,8 +37,8 @@ task flash {
}
runtime {
cpu: select_first([threads, 2])
memory: select_first([memory, 2])
cpu: threads
memory: memory
}
}
\ No newline at end of file
gatk.wdl
+ 75
− 87
View file @ 8fccf548
version 1.0
# Apply Base Quality Score Recalibration (BQSR) model
task ApplyBQSR {
input {
......@@ -14,30 +15,30 @@ task ApplyBQSR {
File refFastaIndex
Int? compressionLevel
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier = 3.0
}
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
ApplyBQSR \
--create-output-bam-md5 \
--add-output-sam-program-record \
-R ~{refFasta} \
-I ~{inputBam} \
--use-original-qualities \
-O ~{outputBamPath} \
-bqsr ~{recalibrationReport} \
--static-quantized-quals 10 --static-quantized-quals 20 --static-quantized-quals 30 \
-L ~{sep=" -L " sequenceGroupInterval}
ApplyBQSR \
--create-output-bam-md5 \
--add-output-sam-program-record \
-R ~{refFasta} \
-I ~{inputBam} \
--use-original-qualities \
-O ~{outputBamPath} \
-bqsr ~{recalibrationReport} \
--static-quantized-quals 10 \
--static-quantized-quals 20 \
--static-quantized-quals 30 \
-L ~{sep=" -L " sequenceGroupInterval}
}
output {
......@@ -46,7 +47,7 @@ task ApplyBQSR {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -66,8 +67,8 @@ task BaseRecalibrator {
File refDict
File refFasta
File refFastaIndex
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier = 3.0
}
Array[File]+ knownIndelsSitesVCFsArg = flatten([
......@@ -79,23 +80,21 @@ task BaseRecalibrator {
select_all([dbsnpVCFindex])
])
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
BaseRecalibrator \
-R ~{refFasta} \
-I ~{inputBam} \
--use-original-qualities \
-O ~{recalibrationReportPath} \
--known-sites ~{sep=" --known-sites " knownIndelsSitesVCFsArg} \
-L ~{sep=" -L " sequenceGroupInterval}
BaseRecalibrator \
-R ~{refFasta} \
-I ~{inputBam} \
--use-original-qualities \
-O ~{recalibrationReportPath} \
--known-sites ~{sep=" --known-sites " knownIndelsSitesVCFsArg} \
-L ~{sep=" -L " sequenceGroupInterval}
}
output {
......@@ -103,7 +102,7 @@ task BaseRecalibrator {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -122,16 +121,14 @@ task CombineGVCFs {
File refFastaIndex
File refDict
Int? compressionLevel
Float? memory
Float? memoryMultiplier
Int? compressionLevel #TODO This isn't being used?
Int memory = 4
Float memoryMultiplier = 3.0
}
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
......@@ -156,7 +153,7 @@ task CombineGVCFs {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -168,15 +165,13 @@ task GatherBqsrReports {
Array[File] inputBQSRreports
String outputReportPath
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier = 3.0
}
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
......@@ -192,7 +187,7 @@ task GatherBqsrReports {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -215,30 +210,27 @@ task GenotypeGVCFs {
File? dbsnpVCFindex
Int? compressionLevel
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier =3.0
}
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
GenotypeGVCFs \
-R ~{refFasta} \
-O ~{outputPath} \
~{"-D " + dbsnpVCF} \
-G StandardAnnotation \
--only-output-calls-starting-in-intervals \
-new-qual \
-V ~{gvcfFiles} \
-L ~{sep=' -L ' intervals}
GenotypeGVCFs \
-R ~{refFasta} \
-O ~{outputPath} \
~{"-D " + dbsnpVCF} \
-G StandardAnnotation \
--only-output-calls-starting-in-intervals \
-new-qual \
-V ~{gvcfFiles} \
-L ~{sep=' -L ' intervals}
}
output {
......@@ -247,13 +239,13 @@ task GenotypeGVCFs {
}
runtime{
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
# Call variants on a single sample with HaplotypeCaller to produce a GVCF
task HaplotypeCallerGvcf {
input {
input {
String? preCommand
Array[File]+ inputBams
Array[File]+ inputBamsIndex
......@@ -262,35 +254,33 @@ task HaplotypeCallerGvcf {
File refDict
File refFasta
File refFastaIndex
Float? contamination
Float contamination = 0.0
Int? compressionLevel
String? gatkJar
File? dbsnpVCF
File? dbsnpVCFindex
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier = 3
}
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
HaplotypeCaller \
-R ~{refFasta} \
-O ~{gvcfPath} \
-I ~{sep=" -I " inputBams} \
-L ~{sep=' -L ' intervalList} \
~{"-D " + dbsnpVCF} \
-contamination ~{default=0 contamination} \
-ERC GVCF
HaplotypeCaller \
-R ~{refFasta} \
-O ~{gvcfPath} \
-I ~{sep=" -I " inputBams} \
-L ~{sep=' -L ' intervalList} \
~{"-D " + dbsnpVCF} \
-contamination ~{contamination} \
-ERC GVCF
}
output {
......@@ -299,7 +289,7 @@ task HaplotypeCallerGvcf {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -316,15 +306,13 @@ task SplitNCigarReads {
String? gatkJar
Array[File]+ intervals
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier = 3
}
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(gatkJar)
then "java -Xmx" + mem + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + gatkJar
else "gatk --java-options -Xmx" + memory + "G"
command {
set -e -o pipefail
......@@ -343,6 +331,6 @@ task SplitNCigarReads {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
htseq.wdl
+ 8
− 8
View file @ 8fccf548
......@@ -6,11 +6,11 @@ task HTSeqCount {
Array[File] alignmentFiles
File gtfFile
String outputTable
String? format
String? order
String? stranded
String format = "bam"
String order = "pos"
String stranded = "no"
Int? memory
Int memory = 3
}
command {
......@@ -18,9 +18,9 @@ task HTSeqCount {
mkdir -p ~{sub(outputTable, basename(outputTable), "")}
~{preCommand}
htseq-count \
-f ~{default="bam" format} \
-r ~{default="pos" order} \
-s ~{default="no" stranded} \
-f ~{format} \
-r ~{order} \
-s ~{stranded} \
~{sep=" " alignmentFiles} \
~{gtfFile} \
> ~{outputTable}
......@@ -31,6 +31,6 @@ task HTSeqCount {
}
runtime {
memory: select_first([memory, 3])
memory: memory
}
}
\ No newline at end of file
macs2.wdl
+ 6
− 6
View file @ 8fccf548
......@@ -6,9 +6,9 @@ task PeakCalling {
Array[File] bamFiles
String outDir
String sampleName
Int? threads
Int? memory
Boolean? nomodel
Int threads = 1
Int memory = 8
Boolean nomodel = false
}
command {
......@@ -18,7 +18,7 @@ task PeakCalling {
--treatment ~{sep = ' ' bamFiles} \
--outdir ~{outDir} \
--name ~{sampleName} \
~{default=false true='--nomodel' false='' nomodel}
~{true='--nomodel' false='' nomodel}
}
output {
......@@ -26,7 +26,7 @@ task PeakCalling {
}
runtime {
cpu: select_first([threads,1])
memory: select_first([memory,8])
cpu: threads
memory: memory
}
}
\ No newline at end of file
ncbi.wdl
+ 17
− 11
View file @ 8fccf548
version 1.0
task genomeDownload {
task GenomeDownload {
input {
String outputPath
String? section = "refseq"
......@@ -12,11 +12,11 @@ task genomeDownload {
String? ncbiBaseUri
Int? parallel
Int? retries
Boolean? verbose=true
Boolean? debug
Boolean verbose = true
Boolean debug = false
String? domain = "all"
String? executable = "ncbi-genome-download"
String executable = "ncbi-genome-download"
String? preCommand
}
......@@ -72,11 +72,11 @@ task genomeDownload {
}
task downloadNtFasta{
task DownloadNtFasta{
input {
String libraryPath
String seqTaxMapPath
Boolean? unzip = true
Boolean unzip = true
String ntDir = libraryPath + "/nt"
String ntFilePath = ntDir + "/nt.fna"
}
......@@ -91,7 +91,8 @@ task downloadNtFasta{
then
zcat ~{ntDir}/nt.gz > ~{ntFilePath}
fi
}
}
output {
File ntFileGz = ntDir + "/nt.gz"
File library = libraryPath
......@@ -102,7 +103,7 @@ task downloadNtFasta{
}
}
task downloadAccessionToTaxId {
task DownloadAccessionToTaxId {
input {
String downloadDir
Boolean gzip = false
......@@ -111,13 +112,18 @@ task downloadAccessionToTaxId {
command {
set -e -o pipefail
mkdir -p ~{downloadDir}
rsync -av --partial rsync://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_*.accession2taxid.gz* ~{downloadDir}
rsync -av \
--partial \
rsync://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/nucl_*.accession2taxid.gz* \
~{downloadDir}
(cd ~{downloadDir} && md5sum -c *.md5)
for file in ~{downloadDir}/nucl_*.accession2taxid.gz
do
zcat $file | tail -n +2 | cut -f 2,3 ~{true="| gzip " false='' gzip}> $file.seqtaxmap~{true='.gz' false='' gzip}
zcat $file | tail -n +2 | cut -f 2,3 ~{true="| gzip" false='' gzip} > \
$file.seqtaxmap~{true='.gz' false='' gzip}
done
}
}
output {
Array[File] seqTaxMaps = glob(downloadDir + "/*.seqtaxmap")
Array[File] seqTaxMapsGz = glob(downloadDir + "/*.seqtaxmap.gz")
......
picard.wdl
+ 70
− 85
View file @ 8fccf548
......@@ -10,29 +10,25 @@ task CollectMultipleMetrics {
File refFastaIndex
String basename
# These should proably be optional, but I'm not sure how to handle the ouput in that
# case (without a null literal).
Boolean collectAlignmentSummaryMetrics = true
Boolean collectInsertSizeMetrics = true
Boolean qualityScoreDistribution = true
Boolean meanQualityByCycle = true
Boolean collectBaseDistributionByCycle = true
Boolean collectGcBiasMetrics = true
#Boolean? rnaSeqMetrics = false # There is a bug in picard https://github.com/broadinstitute/picard/issues/999
#Boolean rnaSeqMetrics = false # There is a bug in picard https://github.com/broadinstitute/picard/issues/999
Boolean collectSequencingArtifactMetrics = true
Boolean collectQualityYieldMetrics = true
String? picardJar
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier = 3.0
}
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "picard -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + picardJar
else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
......@@ -77,7 +73,7 @@ task CollectMultipleMetrics {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -88,19 +84,17 @@ task CollectRnaSeqMetrics {
File bamIndex
File refRefflat
String basename
String? strandSpecificity = "NONE"
String strandSpecificity = "NONE"
String? picardJar
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier = 3.0
}
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "picard -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + picardJar
else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
......@@ -111,7 +105,7 @@ task CollectRnaSeqMetrics {
I=~{bamFile} \
O=~{basename}.RNA_Metrics \
CHART_OUTPUT=~{basename}.RNA_Metrics.pdf \
~{"STRAND_SPECIFICITY=" + strandSpecificity} \
STRAND_SPECIFICITY=~{strandSpecificity} \
REF_FLAT=~{refRefflat}
}
......@@ -121,7 +115,7 @@ task CollectRnaSeqMetrics {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -139,15 +133,13 @@ task CollectTargetedPcrMetrics {
String? picardJar
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier = 3.0
}
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "picard -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + picardJar
else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
......@@ -171,7 +163,7 @@ task CollectTargetedPcrMetrics {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -184,25 +176,23 @@ task GatherBamFiles {
Int? compression_level
String? picardJar
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier = 3.0
}
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "picard -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + picardJar
else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
GatherBamFiles \
INPUT=~{sep=' INPUT=' input_bams} \
OUTPUT=~{output_bam_path} \
CREATE_INDEX=true \
CREATE_MD5_FILE=true
GatherBamFiles \
INPUT=~{sep=' INPUT=' input_bams} \
OUTPUT=~{output_bam_path} \
CREATE_INDEX=true \
CREATE_MD5_FILE=true
}
output {
......@@ -212,7 +202,7 @@ task GatherBamFiles {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -226,8 +216,8 @@ task MarkDuplicates {
Int? compression_level
String? picardJar
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier = 3.0
# The program default for READ_NAME_REGEX is appropriate in nearly every case.
# Sometimes we wish to supply "null" in order to turn off optical duplicate detection
......@@ -238,27 +228,26 @@ task MarkDuplicates {
# Task is assuming query-sorted input so that the Secondary and Supplementary reads get marked correctly
# This works because the output of BWA is query-grouped and therefore, so is the output of MergeBamAlignment.
# While query-grouped isn't actually query-sorted, it's good enough for MarkDuplicates with ASSUME_SORT_ORDER="queryname"
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "picard -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + picardJar
else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
mkdir -p $(dirname ~{output_bam_path})
~{toolCommand} \
MarkDuplicates \
INPUT=~{sep=' INPUT=' input_bams} \
OUTPUT=~{output_bam_path} \
METRICS_FILE=~{metrics_path} \
VALIDATION_STRINGENCY=SILENT \
~{"READ_NAME_REGEX=" + read_name_regex} \
OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 \
CLEAR_DT="false" \
CREATE_INDEX=true \
ADD_PG_TAG_TO_READS=false
MarkDuplicates \
INPUT=~{sep=' INPUT=' input_bams} \
OUTPUT=~{output_bam_path} \
METRICS_FILE=~{metrics_path} \
VALIDATION_STRINGENCY=SILENT \
~{"READ_NAME_REGEX=" + read_name_regex} \
OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 \
CLEAR_DT="false" \
CREATE_INDEX=true \
ADD_PG_TAG_TO_READS=false
}
output {
......@@ -268,7 +257,7 @@ task MarkDuplicates {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -282,25 +271,24 @@ task MergeVCFs {
Int? compressionLevel
String? picardJar
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier = 3.0
}
# Using MergeVcfs instead of GatherVcfs so we can create indices
# See https://github.com/broadinstitute/picard/issues/789 for relevant GatherVcfs ticket
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "picard -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + picardJar
else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
~{toolCommand} \
MergeVcfs \
INPUT=~{sep=' INPUT=' inputVCFs} \
OUTPUT=~{outputVCFpath}
MergeVcfs \
INPUT=~{sep=' INPUT=' inputVCFs} \
OUTPUT=~{outputVCFpath}
}
output {
......@@ -309,7 +297,7 @@ task MergeVCFs {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -320,16 +308,15 @@ task SamToFastq {
String outputRead1
String? outputRead2
String? outputUnpaired
String? picardJar
Float? memory
Float? memoryMultiplier
Int memory = 16 # High memory default to avoid crashes.
Float memoryMultiplier = 3.0
}
Int mem = ceil(select_first([memory, 16.0])) # High memory default to avoid crashes.
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "picard -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + picardJar
else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
......@@ -349,7 +336,7 @@ task SamToFastq {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
......@@ -360,28 +347,26 @@ task ScatterIntervalList {
Int scatter_count
String? picardJar
Float? memory
Float? memoryMultiplier
Int memory = 4
Float memoryMultiplier = 3.0
}
Int mem = ceil(select_first([memory, 4.0]))
String toolCommand = if defined(picardJar)
then "java -Xmx" + mem + "G -jar " + picardJar
else "picard -Xmx" + mem + "G"
then "java -Xmx" + memory + "G -jar " + picardJar
else "picard -Xmx" + memory + "G"
command {
set -e -o pipefail
~{preCommand}
mkdir scatter_list
~{toolCommand} \
IntervalListTools \
SCATTER_COUNT=~{scatter_count} \
SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW \
UNIQUE=true \
SORT=true \
INPUT=~{interval_list} \
OUTPUT=scatter_list
IntervalListTools \
SCATTER_COUNT=~{scatter_count} \
SUBDIVISION_MODE=BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW \
UNIQUE=true \
SORT=true \
INPUT=~{interval_list} \
OUTPUT=scatter_list
}
output {
......@@ -390,6 +375,6 @@ task ScatterIntervalList {
}
runtime {
memory: ceil(mem * select_first([memoryMultiplier, 3.0]))
memory: ceil(memory * memoryMultiplier)
}
}
\ No newline at end of file
}
samtools.wdl
+ 14
− 13
View file @ 8fccf548
......@@ -14,7 +14,9 @@ task Index {
}
output {
File indexFile = if defined(bamIndexPath) then select_first([bamIndexPath]) else bamFilePath + ".bai"
File indexFile = if defined(bamIndexPath)
then select_first([bamIndexPath])
else bamFilePath + ".bai"
}
}
......@@ -73,7 +75,7 @@ task Flagstat {
}
}
task fastq {
task Fastq {
input {
String? preCommand
File inputBam
......@@ -86,9 +88,8 @@ task fastq {
Boolean? appendReadNumber
Boolean? outputQuality
Int? compressionLevel
Int? threads
Int? memory
Int totalThreads = select_first([threads, 1])
Int threads = 1
Int memory = 1
}
command {
......@@ -103,7 +104,7 @@ task fastq {
~{true="-N" false="-n" appendReadNumber} \
~{true="-O" false="" outputQuality} \
~{"-c " + compressionLevel} \
~{"--threads " + totalThreads} \
~{"--threads " + threads} \
~{inputBam}
}
......@@ -114,8 +115,8 @@ task fastq {
}
runtime {
cpu: totalThreads
memory: select_first([memory, 1])
cpu: threads
memory: memory
}
parameter_meta {
......@@ -130,7 +131,7 @@ task fastq {
}
}
task view {
task View {
input {
String? preCommand
File inFile
......@@ -141,8 +142,8 @@ task view {
Int? includeFilter
Int? excludeFilter
Int? excludeSpecificFilter
Int? threads
Int? memory
Int threads = 1
Int memory = 1
}
command {
......@@ -164,7 +165,7 @@ task view {
File outputFile = outputFileName
}
runtime {
cpu: select_first([threads, 1])
memory: select_first([memory, 1])
cpu: threads
memory: memory
}
}
seqtk.wdl
+ 9
− 8
View file @ 8fccf548
version 1.0
task sample {
task Sample {
input {
File sequenceFile
String? outFilePath = "subsampledReads.fq.gz"
String outFilePath = "subsampledReads.fq.gz"
String? preCommand
Int? seed
Boolean? twoPassMode
Boolean twoPassMode
Float? fraction
Int? number
Boolean? zip = true
Boolean zip = true
}
command {
set -e -o pipefail
~{'mkdir -p $(dirname ' + outFilePath + ')'}
mkdir -p $(dirname outFilePath)
~{preCommand}
seqtk sample \
~{"-s " + seed} \
~{true="-2 " false="" twoPassMode} \
~{sequenceFile} \
~{number} ~{fraction} \
~{number} \
~{fraction} \
~{true="| gzip" false="" zip} \
~{"> " + outFilePath}
> ~{outFilePath}
}
output {
File subsampledReads= select_first([outFilePath])
File subsampledReads = outFilePath
}
}
\ No newline at end of file
spades.wdl
+ 23
− 26
View file @ 8fccf548
version 1.0
task spades {
task Spades {
input {
String outputDir
String? preCommand
......@@ -24,18 +24,15 @@ task spades {
Boolean? disableGzipOutput
Boolean? disableRepeatResolution
File? dataset
Int? threads = 1
Float? memoryGb
Int threads = 1
Float memoryGb = 16.0
File? tmpDir
String? k
Float? covCutoff
Int? phredOffset
}
Int finalThreads = select_first([threads])
Float totalMemory = select_first([memoryGb, finalThreads * 16.0])
Int finalMemory = ceil(totalMemory)
Int clusterMemory = ceil(totalMemory / finalThreads)
Int clusterMemory = ceil(memoryGb / threads)
command {
set -e -o pipefail
......@@ -47,26 +44,26 @@ task spades {
~{true="--rna" false="" rna} \
~{true="--plasmid" false="" plasmid} \
~{true="--iontorrent" false="" ionTorrent} \
~{"--12 " + interlacedReads } \
~{"--12 " + interlacedReads} \
~{true="-1" false="-s" defined(read2)} ~{read1} \
~{"-2 " + read2 } \
~{"--sanger " + sangerReads } \
~{"--pacbio " + pacbioReads } \
~{"--nanopore " + nanoporeReads } \
~{"--tslr " + tslrContigs } \
~{"--trusted-contigs " + trustedContigs } \
~{"--untrusted-contigs " + untrustedContigs } \
~{true="--only-error-correction" false="" onlyErrorCorrection } \
~{true="--only-assembler" false="" onlyAssembler } \
~{true="--careful" false="" careful } \
~{"-2 " + read2} \
~{"--sanger " + sangerReads} \
~{"--pacbio " + pacbioReads} \
~{"--nanopore " + nanoporeReads} \
~{"--tslr " + tslrContigs} \
~{"--trusted-contigs " + trustedContigs} \
~{"--untrusted-contigs " + untrustedContigs} \
~{true="--only-error-correction" false="" onlyErrorCorrection} \
~{true="--only-assembler" false="" onlyAssembler} \
~{true="--careful" false="" careful} \
~{true="--disable-gzip-output" false="" disableGzipOutput} \
~{true="--disable-rr" false="" disableRepeatResolution } \
~{"--dataset " + dataset } \
~{"--threads " + finalThreads} \
~{"--memory " + finalMemory } \
~{"-k " + k } \
~{"--cov-cutoff " + covCutoff } \
~{"--phred-offset " + phredOffset }
~{true="--disable-rr" false="" disableRepeatResolution} \
~{"--dataset " + dataset} \
~{"--threads " + threads} \
~{"--memory " + memoryGb} \
~{"-k " + k} \
~{"--cov-cutoff " + covCutoff} \
~{"--phred-offset " + phredOffset}
}
output {
......@@ -82,7 +79,7 @@ task spades {
}
runtime {
cpu: finalThreads
cpu: threads
memory: clusterMemory
}
}
\ No newline at end of file
star.wdl
+ 12
− 15
View file @ 8fccf548
......@@ -9,23 +9,20 @@ task Star {
String genomeDir
String outFileNamePrefix
String? outSAMtype
String? readFilesCommand
Int? runThreadN
String outSAMtype = "BAM SortedByCoordinate"
String readFilesCommand = "zcat"
Int runThreadN = 1
String? outStd
String? twopassMode
Array[String]? outSAMattrRGline
Int? limitBAMsortRAM
Int? memory
Int memory = 10
}
#TODO needs to be extended for all possible output extensions
Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"}
# converts String? to String for use as key (for the Map above) in output
String key = select_first([outSAMtype, "BAM SortedByCoordinate"])
command {
set -e -o pipefail
mkdir -p ~{sub(outFileNamePrefix, basename(outFileNamePrefix) + "$", "")}
......@@ -34,8 +31,8 @@ task Star {
--readFilesIn ~{sep=',' inputR1} ~{sep="," inputR2} \
--outFileNamePrefix ~{outFileNamePrefix} \
--genomeDir ~{genomeDir} \
--outSAMtype ~{default="BAM SortedByCoordinate" outSAMtype} \
--readFilesCommand ~{default="zcat" readFilesCommand} \
--outSAMtype ~{outSAMtype} \
--readFilesCommand ~{readFilesCommand} \
~{"--runThreadN " + runThreadN} \
~{"--outStd " + outStd} \
~{"--twopassMode " + twopassMode} \
......@@ -44,25 +41,25 @@ task Star {
}
output {
File bamFile = outFileNamePrefix + "Aligned." + samOutputNames[key]
File bamFile = outFileNamePrefix + "Aligned." + samOutputNames[outSAMtype]
}
runtime {
cpu: select_first([runThreadN, 1])
memory: select_first([memory, 10])
cpu: runThreadN
memory: memory
}
}
task makeStarRGline {
task MakeStarRGline {
input {
String sample
String library
String? platform
String platform = "ILLUMINA"
String readgroup
}
command {
printf '"ID:~{readgroup}" "LB:~{library}" "PL:~{default="ILLUMINA" platform}" "SM:~{sample}"'
printf '"ID:~{readgroup}" "LB:~{library}" "PL:~{platform}" "SM:~{sample}"'
}
output {
......
stringtie.wdl
+ 2
− 2
View file @ 8fccf548
......@@ -5,7 +5,7 @@ task Stringtie {
String? preCommand
File alignedReads
File? referenceGtf
Int? threads
Int threads = 1
String assembledTranscriptsFile
Boolean? firstStranded
Boolean? secondStranded
......@@ -32,6 +32,6 @@ task Stringtie {
}
runtime {
cpu: select_first([threads, 1])
cpu: threads
}
}
\ No newline at end of file
unicycler.wdl
+ 5
− 5
View file @ 8fccf548
version 1.0
task unicycler {
task Unicycler {
input {
String? preCommand
File? short1
......@@ -12,8 +12,8 @@ task unicycler {
Int? minFastaLength
Int? keep
Boolean? vcf
Int? threads = 1
Int? memory = 4
Int threads = 1
Int memory = 4
String? mode
Float? minBridgeQual
Int? linearSeqs
......@@ -101,7 +101,7 @@ task unicycler {
}
runtime {
cpu: select_first([threads])
memory: select_first([memory])
cpu: threads
memory: memory
}
}
\ No newline at end of file
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