diff --git a/biopet.wdl b/biopet.wdl
index 545d6922f3f0391474b04943c3ccde713ab9ce92..9b9722cfa0de8b17c4ab51bc60d9f8d6838ebb3d 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -12,8 +12,8 @@ task BaseCounter {
Float? memory
Float? memoryMultiplier
-
Int mem = ceil(select_first([memory, 12.0]))
+
command {
set -e -o pipefail
mkdir -p ${outputDir}
@@ -67,6 +67,53 @@ task BaseCounter {
}
}
+task extractAdaptersFastqc {
+ File? toolJar
+ File inputFile
+ String outputDir
+ 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 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"
+
+ command {
+ set -e
+ 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]))
+ }
+
+ runtime {
+ memory: ceil(mem * select_first([memoryMultiplier, 2.5]))
+ }
+}
+
+
task FastqSplitter {
String? preCommand
File inputFastq
@@ -99,12 +146,13 @@ task FastqSync {
File in2
String out1path
String out2path
- File tool_jar
+ File toolJar
+
command {
set -e -o pipefail
${preCommand}
mkdir -p $(dirname ${out1path}) $(dirname ${out2path})
- java -jar ${tool_jar} \
+ java -jar ${toolJar} \
--in1 ${in1} \
--in2 ${in2} \
--ref1 ${ref1} \
@@ -112,6 +160,7 @@ task FastqSync {
--out1 ${out1path} \
--out2 ${out2path}
}
+
output {
File out1 = out1path
File out2 = out2path
@@ -120,7 +169,7 @@ task FastqSync {
task SampleConfig {
String? preCommand
- String tool_jar
+ File toolJar
Array[File]+ inputFiles
String keyFilePath
String? sample
@@ -131,13 +180,13 @@ task SampleConfig {
Float? memory
Float? memoryMultiplier
-
Int mem = ceil(select_first([memory, 4.0]))
+
command {
set -e -o pipefail
${preCommand}
mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"}
- java -Xmx${mem}G -jar ${tool_jar} \
+ java -Xmx${mem}G -jar ${toolJar} \
-i ${sep="-i " inputFiles} \
${"--sample " + sample} \
${"--library " + library} \
@@ -160,23 +209,23 @@ task SampleConfig {
task ScatterRegions {
String? preCommand
- File ref_fasta
- File ref_dict
+ File refFasta
+ File refDict
String outputDirPath
- String tool_jar
+ File toolJar
Int? scatterSize
File? regions
Float? memory
Float? memoryMultiplier
-
Int mem = ceil(select_first([memory, 4.0]))
+
command {
set -e -o pipefail
${preCommand}
mkdir -p ${outputDirPath}
- java -Xmx${mem}G -jar ${tool_jar} \
- -R ${ref_fasta} \
+ java -Xmx${mem}G -jar ${toolJar} \
+ -R ${refFasta} \
-o ${outputDirPath} \
${"-s " + scatterSize} \
${"-L " + regions}
diff --git a/centrifuge.wdl b/centrifuge.wdl
index 09d2ee79b45c7b4bcd284a35cf0b5b3c1154df04..e950284b5076276bfc6f189ecc2819be1096e665 100644
--- a/centrifuge.wdl
+++ b/centrifuge.wdl
@@ -1,8 +1,7 @@
# Copyright Sequencing Analysis Support Core - Leiden University Medical Center 2018
#
# Tasks from centrifuge
-task build {
-
+task Build {
File conversionTable
File taxonomyTree
File inputFasta
@@ -22,9 +21,10 @@ task build {
File? nameTable
File? sizeTable
Int? seed
+ Int? kmerCount
+
Int? threads
Int? memory
- Int? kmerCount
command {
set -e -o pipefail
@@ -56,25 +56,28 @@ task build {
}
}
-task classify {
+task Classify {
String outputDir
Boolean? compressOutput = true
String? preCommand
String indexPrefix
- File? unpairedReads
- File read1
- File? read2
+ Array[File]? unpairedReads
+ Array[File]+ read1
+ Array[File]? read2
Boolean? fastaInput
# Variables for handling output
- String outputFileName = outputDir + "/centrifuge.out"
- String reportFileName = outputDir + "/centrifuge_report.tsv"
- String finalOutputName = if (compressOutput == true) then outputFileName + ".gz" else outputFileName
- String? metFileName # If this is specified, the report file is empty
+ String outputFilePath = outputDir + "/centrifuge.out"
+ String reportFilePath = outputDir + "/centrifuge_report.tsv"
+ String finalOutputPath = if (compressOutput == true)
+ then outputFilePath + ".gz"
+ else outputFilePath
+ String? metFilePath # If this is specified, the report file is empty
Int? assignments
Int? minHitLen
Int? minTotalLen
Array[String]? hostTaxIds
Array[String]? excludeTaxIds
+
Int? threads
Int? memory
@@ -86,22 +89,22 @@ task classify {
${"-p " + threads} \
${"-x " + indexPrefix} \
${true="-f" false="" fastaInput} \
- ${true="-k " false="" defined(assignments)} ${assignments} \
- ${true="-1 " false="-U " defined(read2)} ${read1} \
- ${"-2 " + read2} \
- ${"-U " + unpairedReads} \
- ${"--report-file " + reportFileName} \
+ ${true="-k" false="" defined(assignments)} ${assignments} \
+ ${true="-1" false="-U" defined(read2)} ${sep=',' read1} \
+ ${true="-2" false="" defined(read2)} ${sep=',' read2} \
+ ${true="-U" false="" defined(unpairedReads)} ${sep=',' unpairedReads} \
+ ${"--report-file " + reportFilePath} \
${"--min-hitlen " + minHitLen} \
${"--min-totallen " + minTotalLen} \
- ${"--met-file " + metFileName} \
+ ${"--met-file " + metFilePath} \
${true="--host-taxids " false="" defined(hostTaxIds)} ${sep=',' hostTaxIds} \
${true="--exclude-taxids " false="" defined(excludeTaxIds)} ${sep=',' excludeTaxIds} \
- ${true="| gzip -c >" false="-S" compressOutput} ${finalOutputName}
+ ${true="| gzip -c >" false="-S" compressOutput} ${finalOutputPath}
}
output {
- File classifiedReads = finalOutputName
- File reportFile = reportFileName
+ File classifiedReads = finalOutputPath
+ File reportFile = reportFilePath
}
runtime {
@@ -110,7 +113,7 @@ task classify {
}
}
-task download {
+task Download {
String libraryPath
Array[String]? domain
String? executable = "centrifuge-download"
@@ -153,10 +156,11 @@ task download {
}
}
-task downloadTaxonomy {
+task DownloadTaxonomy {
String centrifugeTaxonomyDir
String? executable = "centrifuge-download"
String? preCommand
+
command {
set -e -o pipefail
${preCommand}
@@ -164,23 +168,28 @@ task downloadTaxonomy {
-o ${centrifugeTaxonomyDir} \
taxonomy
}
+
output {
File taxonomyTree = centrifugeTaxonomyDir + "/nodes.dmp"
File nameTable = centrifugeTaxonomyDir + "/names.dmp"
}
}
-task kreport {
+task Kreport {
String? preCommand
File centrifugeOut
Boolean inputIsCompressed
- String kreportFileName=sub(centrifugeOut, "\\.out$|\\.out\\.gz$", "\\.kreport")
+ String outputDir
+ String? suffix = "kreport"
+ String? prefix = "centrifuge"
+ String kreportFilePath = outputDir + "/" + prefix + "." + suffix
String indexPrefix
Boolean? onlyUnique
Boolean? showZeros
Boolean? isCountTable
Int? minScore
Int? minLength
+
Int? cores
Int? memory
@@ -196,11 +205,11 @@ task kreport {
${"--min-length " + minLength} \
${true="<(zcat" false="" inputIsCompressed} ${centrifugeOut}\
${true=")" false="" inputIsCompressed} \
- > ${kreportFileName}
+ > ${kreportFilePath}
}
output {
- File kreport = kreportFileName
+ File kreport = kreportFilePath
}
runtime {
diff --git a/fastqc.wdl b/fastqc.wdl
index f0fd2fec0371432f054aecd9624dc9bda628f292..d9135f73197bf1e985f5a096c45f449f37e42d94 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -55,48 +55,6 @@ task fastqc {
}
}
-task extractAdapters {
- File extractAdaptersFastqcJar
- File inputFile
- String outputDir
- 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 mem = ceil(select_first([memory, 4.0]))
- command {
- set -e
- mkdir -p ${outputDir}
- java -Xmx${mem}G -jar ${extractAdaptersFastqcJar} \
- --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]))
- }
-
- runtime {
- memory: ceil(mem * select_first([memoryMultiplier, 2.5]))
- }
-}
-
task getConfiguration {
String? preCommand
String? fastqcDirFile = "fastqcDir.txt"