centrifuge to 1.0

centrifuge.wdl

+version 1.0
 # Copyright Sequencing Analysis Support Core - Leiden University Medical Center 2018
 #
 # Tasks from centrifuge
 task Build {
-    File conversionTable
-    File taxonomyTree
-    File inputFasta
-    String centrifugeIndexBase
-    String? preCommand
-    String? centrifugeBuildExecutable = "centrifuge-build"
-    #Boolean? c = false
-    Boolean? largeIndex = false
-    Boolean? noAuto = false
-    Int? bMax
-    Int? bMaxDivn
-    Boolean? noDiffCover = false
-    Boolean? noRef = false
-    Boolean? justRef = false
-    Int? offRate
-    Int? fTabChars
-    File? nameTable
-    File? sizeTable
-    Int? seed
-    Int? kmerCount
-
-    Int? threads
-    Int? memory
-
+    input {
+        File conversionTable
+        File taxonomyTree
+        File inputFasta
+        String centrifugeIndexBase
+        String? preCommand
+        String? centrifugeBuildExecutable = "centrifuge-build"
+        #Boolean? c = false
+        Boolean? largeIndex = false
+        Boolean? noAuto = false
+        Int? bMax
+        Int? bMaxDivn
+        Boolean? noDiffCover = false
+        Boolean? noRef = false
+        Boolean? justRef = false
+        Int? offRate
+        Int? fTabChars
+        File? nameTable
+        File? sizeTable
+        Int? seed
+        Int? kmerCount
+
+        Int? threads
+        Int? memory
+    }
     command {
         set -e -o pipefail
-        ${preCommand}
-        ${"mkdir -p $(dirname " + centrifugeIndexBase + ")"}
-        ${centrifugeBuildExecutable} \
-        ${true='--large-index' false='' largeIndex} \
-        ${true='--noauto' false='' noAuto} \
-        ${'--bmax ' + bMax} \
-        ${'--bmaxdivn ' + bMaxDivn} \
-        ${true='--nodc' false='' noDiffCover} \
-        ${true='--noref' false='' noRef} \
-        ${true='--justref' false='' justRef} \
-        ${'--offrate ' + offRate} \
-        ${'--ftabchars ' + fTabChars} \
-        ${'--name-table ' + nameTable } \
-        ${'--size-table ' + sizeTable} \
-        ${'--seed ' + seed} \
-        ${'--kmer-count' + kmerCount} \
-        ${'--threads ' + threads} \
-        --conversion-table ${conversionTable} \
-        --taxonomy-tree ${taxonomyTree} \
-        ${inputFasta} \
-        ${centrifugeIndexBase}
+        ~{preCommand}
+        ~{"mkdir -p $(dirname " + centrifugeIndexBase + ")"}
+        ~{centrifugeBuildExecutable} \
+        ~{true='--large-index' false='' largeIndex} \
+        ~{true='--noauto' false='' noAuto} \
+        ~{'--bmax ' + bMax} \
+        ~{'--bmaxdivn ' + bMaxDivn} \
+        ~{true='--nodc' false='' noDiffCover} \
+        ~{true='--noref' false='' noRef} \
+        ~{true='--justref' false='' justRef} \
+        ~{'--offrate ' + offRate} \
+        ~{'--ftabchars ' + fTabChars} \
+        ~{'--name-table ' + nameTable } \
+        ~{'--size-table ' + sizeTable} \
+        ~{'--seed ' + seed} \
+        ~{'--kmer-count' + kmerCount} \
+        ~{'--threads ' + threads} \
+        --conversion-table ~{conversionTable} \
+        --taxonomy-tree ~{taxonomyTree} \
+        ~{inputFasta} \
+        ~{centrifugeIndexBase}
     }
     runtime {
         cpu: select_first([threads, 8])
@@ -57,49 +59,53 @@ task Build {
 }
 
 task Classify {
-    String outputDir
-    Boolean? compressOutput = true
-    String? preCommand
-    String indexPrefix
-    Array[File]? unpairedReads
-    Array[File]+ read1
-    Array[File]? read2
-    Boolean? fastaInput
-    # Variables for handling output
+    input {
+        String outputDir
+        Boolean? compressOutput = true
+        String? preCommand
+        String indexPrefix
+        Array[File]? unpairedReads
+        Array[File]+ read1
+        Array[File]? read2
+        Boolean? fastaInput
+        # Variables for handling output
+
+        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
+    }
+
     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
 
     command {
         set -e -o pipefail
-        mkdir -p ${outputDir}
-        ${preCommand}
+        mkdir -p ~{outputDir}
+        ~{preCommand}
         centrifuge \
-        ${"-p " + select_first([threads, 4])} \
-        ${"-x " + indexPrefix} \
-        ${true="-f" false="" fastaInput} \
-        ${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 " + metFilePath} \
-        ${true="--host-taxids " false="" defined(hostTaxIds)} ${sep=',' hostTaxIds} \
-        ${true="--exclude-taxids " false="" defined(excludeTaxIds)} ${sep=',' excludeTaxIds} \
-        ${true="| gzip -c >" false="-S" compressOutput} ${finalOutputPath}
+        ~{"-p " + select_first([threads, 4])} \
+        ~{"-x " + indexPrefix} \
+        ~{true="-f" false="" fastaInput} \
+        ~{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 " + metFilePath} \
+        ~{true="--host-taxids " false="" defined(hostTaxIds)} ~{sep=',' hostTaxIds} \
+        ~{true="--exclude-taxids " false="" defined(excludeTaxIds)} ~{sep=',' excludeTaxIds} \
+        ~{true="| gzip -c >" false="-S" compressOutput} ~{finalOutputPath}
     }
 
     output {
@@ -114,58 +120,60 @@ task Classify {
 }
 
 task Download {
-    String libraryPath
-    Array[String]? domain
-    String? executable = "centrifuge-download"
-    String? preCommand
-    String? seqTaxMapPath
-    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
-
+        input {
+        String libraryPath
+        Array[String]? domain
+        String? executable = "centrifuge-download"
+        String? preCommand
+        String? seqTaxMapPath
+        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
+    }
     # This will use centrifuge-download to download.
     # The bash statement at the beginning is to make sure
     # the directory for the SeqTaxMapPath exists.
     command {
         set -e -o pipefail
-        ${preCommand}
-        ${"mkdir -p $(dirname " + seqTaxMapPath + ")"}
-        ${executable} \
-        -o ${libraryPath} \
-        ${true='-d ' false='' defined(domain)}${sep=','  domain} \
-        ${'-a "' + assemblyLevel + '"'} \
-        ${"-c " + refseqCategory} \
-        ${true='-t' false='' defined(taxIds)} '${sep=',' taxIds}' \
-        ${true='-r' false='' downloadRnaSeqs} \
-        ${true='-u' false='' filterUnplaced} \
-        ${true='-m' false='' maskLowComplexRegions} \
-        ${true='-l' false='' modifyHeader} \
-        ${true='-g' false='' downloadGiMap} \
-        ${database} ${">> " + seqTaxMapPath}
+        ~{preCommand}
+        ~{"mkdir -p $(dirname " + seqTaxMapPath + ")"}
+        ~{executable} \
+        -o ~{libraryPath} \
+        ~{true='-d ' false='' defined(domain)}~{sep=','  domain} \
+        ~{'-a "' + assemblyLevel + '"'} \
+        ~{"-c " + refseqCategory} \
+        ~{true='-t' false='' defined(taxIds)} '~{sep=',' taxIds}' \
+        ~{true='-r' false='' downloadRnaSeqs} \
+        ~{true='-u' false='' filterUnplaced} \
+        ~{true='-m' false='' maskLowComplexRegions} \
+        ~{true='-l' false='' modifyHeader} \
+        ~{true='-g' false='' downloadGiMap} \
+        ~{database} ~{">> " + seqTaxMapPath}
     }
     output {
-        File seqTaxMap = "${seqTaxMapPath}"
+        File seqTaxMap = "~{seqTaxMapPath}"
         File library = libraryPath
         Array[File] fastaFiles = glob(libraryPath + "/*/*.fna")
     }
  }
 
 task DownloadTaxonomy {
-    String centrifugeTaxonomyDir
-    String? executable = "centrifuge-download"
-    String? preCommand
-
+    input {
+        String centrifugeTaxonomyDir
+        String? executable = "centrifuge-download"
+        String? preCommand
+    }
     command {
         set -e -o pipefail
-        ${preCommand}
-        ${executable} \
-        -o ${centrifugeTaxonomyDir} \
+        ~{preCommand}
+        ~{executable} \
+        -o ~{centrifugeTaxonomyDir} \
         taxonomy
     }
 
@@ -176,36 +184,37 @@ task DownloadTaxonomy {
  }
 
 task Kreport {
-    String? preCommand
-    File centrifugeOut
-    Boolean inputIsCompressed
-    String outputDir
-    String? suffix = "kreport"
-    String? prefix = "centrifuge"
+    input {
+        String? preCommand
+        File centrifugeOut
+        Boolean inputIsCompressed
+        String outputDir
+        String? suffix = "kreport"
+        String? prefix = "centrifuge"
+        String indexPrefix
+        Boolean? onlyUnique
+        Boolean? showZeros
+        Boolean? isCountTable
+        Int? minScore
+        Int? minLength
+
+        Int? cores
+        Int? memory
+    }
     String kreportFilePath = outputDir + "/" + prefix + "." + suffix
-    String indexPrefix
-    Boolean? onlyUnique
-    Boolean? showZeros
-    Boolean? isCountTable
-    Int? minScore
-    Int? minLength
-
-    Int? cores
-    Int? memory
-
     command {
         set -e -o pipefail
-        ${preCommand}
+        ~{preCommand}
         centrifuge-kreport \
-        -x ${indexPrefix} \
-        ${true="--only-unique" false="" onlyUnique} \
-        ${true="--show-zeros" false="" showZeros} \
-        ${true="--is-count-table" false="" isCountTable} \
-        ${"--min-score " + minScore} \
-        ${"--min-length " + minLength} \
-        ${true="<(zcat" false="" inputIsCompressed} ${centrifugeOut}\
-        ${true=")" false="" inputIsCompressed} \
-        > ${kreportFilePath}
+        -x ~{indexPrefix} \
+        ~{true="--only-unique" false="" onlyUnique} \
+        ~{true="--show-zeros" false="" showZeros} \
+        ~{true="--is-count-table" false="" isCountTable} \
+        ~{"--min-score " + minScore} \
+        ~{"--min-length " + minLength} \
+        ~{true="<(zcat" false="" inputIsCompressed} ~{centrifugeOut}\
+        ~{true=")" false="" inputIsCompressed} \
+        > ~{kreportFilePath}
     }
 
     output {