diff --git a/bioconda.wdl b/bioconda.wdl
index e0b56b4a1df922c33015b3e357a804c338b03ca6..0a513ddc5df99f1354cfd8a4db8aad75d8ef7428 100644
--- a/bioconda.wdl
+++ b/bioconda.wdl
@@ -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 \
diff --git a/biopet.wdl b/biopet.wdl
index 3b550be223a7441a70eb8c4b21463b34005500c3..36d6f2a9cd7b4b4bf633a063ff2220c2cee70995 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)
}
}
@@ -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 d012b38ea8e94bcd4d54e992cd43315e6df3ddb5..01d1b7d08b798083d0bb7dbf6fd74ce4ebe64a14 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -1,6 +1,6 @@
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
diff --git a/centrifuge.wdl b/centrifuge.wdl
index a6659775f49748069a5f06ccec9961d938d549a0..4b128c33627eb4eec4facb184c4e49a321d4b4a7 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -1,4 +1,5 @@
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
}
}
diff --git a/common.wdl b/common.wdl
index 581553ad71957985b0e3fa5541c6d0f3f26c122f..15e99f5804089fdd328f263b21804dc18712e752 100644
--- a/common.wdl
+++ b/common.wdl
@@ -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 {
diff --git a/cutadapt.wdl b/cutadapt.wdl
index 4a09e0dd144013cceec4f13b92ed180e77e0a51b..8b073442c02a449871f7dc6a320a8eabdf82d8d4 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -1,6 +1,6 @@
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
}
}
diff --git a/fastqc.wdl b/fastqc.wdl
index 4ca2733c53e2df4ddc58fec3a22081340d20ee52..6d924cf550a84640fcf3e8f9e1b555d2cf239dd7 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -1,6 +1,6 @@
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 {
diff --git a/flash.wdl b/flash.wdl
index 93ba4cd92b4f3d16a6e209c1fca9c6972b6052d9..3d3eecdf3820be7c841ca44f0f4de580df5e61d1 100644
--- a/flash.wdl
+++ b/flash.wdl
@@ -1,17 +1,17 @@
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
diff --git a/gatk.wdl b/gatk.wdl
index c8ea6e7d1e484e4afa334981ca8864b58b3d7d10..68281f386d0dab5e69f734415711a570f657382b 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -1,4 +1,5 @@
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)
}
}
diff --git a/htseq.wdl b/htseq.wdl
index 87c4c676fe5ea2485837449b0d802ea52e927fe4..db399cc2fb35061e69d280eb2efbcf44e1ccfb6d 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -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
diff --git a/macs2.wdl b/macs2.wdl
index fb580348dbad6f6f10fba2f48d68545a25fd49b2..8edcabab08bcbb6ec3fc3310d0968ebacfc1550e 100644
--- a/macs2.wdl
+++ b/macs2.wdl
@@ -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
diff --git a/ncbi.wdl b/ncbi.wdl
index b6e0deb6f2008d6b238595c85779f31955788615..0678d3d4ea2fffcb9207e972779d056679058fe0 100644
--- a/ncbi.wdl
+++ b/ncbi.wdl
@@ -1,6 +1,6 @@
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")
diff --git a/picard.wdl b/picard.wdl
index 71f566e8ad0591da14d0848a2acfd4e583e211ad..0b13ebe4dbf857f311d5f5836e668ebd0545d62d 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -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
+}
diff --git a/samtools.wdl b/samtools.wdl
index d756fda3367a89c7a8f97d9ede216f45592bcce8..2d910379db88bb9402df50c2e0704e08263a9ff7 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -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
}
}
diff --git a/seqtk.wdl b/seqtk.wdl
index d55fa716a993525a68d0559ad97462d31de513af..64c604a5ecfe0beba399605dcabb1bb3de0ee59a 100644
--- a/seqtk.wdl
+++ b/seqtk.wdl
@@ -1,31 +1,32 @@
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
diff --git a/spades.wdl b/spades.wdl
index 57bc6eb83ef5b6f5cbd30778f54b9c92c6e03451..47195f196967b8b1863b908d9c483ed49df9f978 100644
--- a/spades.wdl
+++ b/spades.wdl
@@ -1,6 +1,6 @@
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
diff --git a/star.wdl b/star.wdl
index 1301fe145daaf9d79c7055e5cea7d30dcc322e4d..e03f6301052b648f2b86cd126e5ecfd9bdd27aed 100644
--- a/star.wdl
+++ b/star.wdl
@@ -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 {
diff --git a/stringtie.wdl b/stringtie.wdl
index 9929b8062aa9edb17a7fa3d832529794938e6b8d..97455da498f722ddf05008fc7102c9eef360335e 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -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
diff --git a/unicycler.wdl b/unicycler.wdl
index 318252ae25ef8c94ab10e2f6cab7bfca5476971a..c5b30ba93c184a1aef7417e16997053ca507101e 100644
--- a/unicycler.wdl
+++ b/unicycler.wdl
@@ -1,6 +1,6 @@
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