Merge branch 'master' into BIOWDL-25

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}

centrifuge.wdl

 # 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 {

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"