added stylish newlines

bioconda.wdl

@@ -9,6 +9,7 @@ task installPrefix {
         String prefix
         String? condaPath
     }
+
     command <<<
         ~{default="conda" condaPath} create \
         --json -q \
@@ -21,6 +22,7 @@ task installPrefix {
         --prefix ${prefix} \
         ~{sep=' ' requirements}
     >>>
+
     output {
         File condaEnvPath=prefix
         File condaJson=stdout()

biopet.wdl

@@ -89,6 +89,7 @@ task ExtractAdaptersFastqc {
         Float? memory
         Float? memoryMultiplier
     }
+
     Int mem = ceil(select_first([memory, 4.0]))
 
     String toolCommand = if defined(toolJar)
@@ -174,6 +175,7 @@ task FastqSync {
         Float? memory
         Float? memoryMultiplier
     }
+
     Int mem = ceil(select_first([memory, 4.0]))
 
     String toolCommand = if defined(toolJar)
@@ -297,6 +299,7 @@ task Seqstat {
         Float? memory
         Float? memoryMultiplier
     }
+
     Int mem = ceil(select_first([memory, 4.0]))
 
     String toolCommand = if defined(toolJar)
@@ -331,6 +334,7 @@ task ValidateAnnotation {
         Float? memory
         Float? memoryMultiplier
     }
+
     Int mem = ceil(select_first([memory, 4.0]))
 
     String toolCommand = if defined(toolJar)
@@ -365,6 +369,7 @@ task ValidateFastq {
         Float? memory
         Float? memoryMultiplier
     }
+
     Int mem = ceil(select_first([memory, 4.0]))
 
     String toolCommand = if defined(toolJar)
@@ -398,6 +403,7 @@ task ValidateVcf {
         Float? memory
         Float? memoryMultiplier
     }
+
     Int mem = ceil(select_first([memory, 4.0]))
 
     String toolCommand = if defined(toolJar)

bwa.wdl

@@ -26,6 +26,7 @@ task mem {
     output {
         File bamFile = outputPath
     }
+
     runtime{
         cpu: select_first([threads,1])
         memory: select_first([memory,8])
@@ -62,6 +63,7 @@ task index {
         File indexedFasta = outputFile
         Array[File] indexFiles = [outputFile + ".bwt",outputFile + ".pac",outputFile + ".sa",outputFile + ".amb",outputFile + ".ann"]
     }
+
     parameter_meta {
         fasta: "Fasta file to be indexed"
         constructionAlgorithm: "-a STR    BWT construction algorithm: bwtsw, is or rb2 [auto]"

centrifuge.wdl

@@ -28,6 +28,7 @@ task Build {
         Int? threads
         Int? memory
     }
+
     command {
         set -e -o pipefail
         ~{preCommand}
@@ -52,6 +53,7 @@ task Build {
         ~{inputFasta} \
         ~{centrifugeIndexBase}
     }
+
     runtime {
         cpu: select_first([threads, 8])
         memory: select_first([memory, 20])
@@ -136,6 +138,7 @@ task Download {
         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.
@@ -201,6 +204,7 @@ task Kreport {
         Int? cores
         Int? memory
     }
+
     String kreportFilePath = outputDir + "/" + prefix + "." + suffix
     command {
         set -e -o pipefail

common.wdl

@@ -5,6 +5,7 @@ task AppendToStringArray {
         Array[String] array
         String string
     }
+
     command {
         echo "~{sep='\n' array}
         ~{string}"
@@ -25,6 +26,7 @@ task CheckFileMD5 {
         File file
         String MD5sum
     }
+
     command {
         set -e -o pipefail
         MD5SUM=$(md5sum ~{file} | cut -d ' ' -f 1)
@@ -39,6 +41,7 @@ task ConcatenateTextFiles {
         Boolean? unzip = false
         Boolean? zip = false
     }
+
     command {
         set -e -o pipefail
         ~{"mkdir -p $(dirname " + combinedFilePath + ")"}
@@ -62,6 +65,7 @@ task CreateLink {
         String inputFile
         String outputPath
     }
+
     command {
         ln -sf ~{inputFile} ~{outputPath}
     }
@@ -98,6 +102,7 @@ task ObjectMd5 {
     input {
         Object the_object
     }
+
     command {
         cat ~{write_object(the_object)} |  md5sum - | sed -e 's/  -//'
     }
@@ -115,6 +120,7 @@ task StringArrayMd5 {
     input {
         Array[String] stringArray
     }
+
     command {
         set -eu -o pipefail
         echo ~{sep=',' stringArray} | md5sum - | sed -e 's/  -//'

cutadapt.wdl

@@ -60,6 +60,7 @@ task cutadapt {
         Boolean? noZeroCap
         String? reportPath
     }
+
     command {
         set -e -o pipefail
         ~{"mkdir -p $(dirname " + read1output + ")"}
@@ -107,6 +108,7 @@ task cutadapt {
         ~{true="--zero-cap" false="" zeroCap} ~{true="--no-zero-cap" false="" noZeroCap} \
         ~{read1} ~{read2} ~{"> " + reportPath}
     }
+
     output{
         File report = if defined(reportPath) then select_first([reportPath]) else stdout()
         File cutRead1 = read1output
@@ -121,6 +123,7 @@ task cutadapt {
         File? restFile=restFilePath
         File? wildcardFile=wildcardFilePath
     }
+
     runtime {
         cpu: select_first([cores])
         memory: select_first([memory])

fastqc.wdl

@@ -19,6 +19,7 @@ task fastqc {
         Int? kmers
         String? dir
     }
+
     # Chops of the .gz extension if present.
     String name = sub(seqFile, "\\.gz$","")
     # This regex chops of the extension and replaces it with _fastqc for the reportdir.
@@ -64,6 +65,7 @@ task getConfiguration {
         String? preCommand
         String? fastqcDirFile = "fastqcDir.txt"
     }
+
     command {
         set -e -o pipefail
         ~{preCommand}

gatk.wdl

@@ -272,6 +272,7 @@ task HaplotypeCallerGvcf {
         Float? memory
         Float? memoryMultiplier
     }
+
     Int mem = ceil(select_first([memory, 4.0]))
 
     String toolCommand = if defined(gatkJar)
@@ -318,6 +319,7 @@ task SplitNCigarReads {
         Float? memory
         Float? memoryMultiplier
     }
+
     Int mem = ceil(select_first([memory, 4.0]))
 
     String toolCommand = if defined(gatkJar)

macs2.wdl

@@ -10,6 +10,7 @@ task PeakCalling {
         Int? memory
         Boolean? nomodel
     }
+
     command {
         set -e -o pipefail
         ~{preCommand}

mergecounts.wdl

@@ -10,6 +10,7 @@ task MergeCounts {
         Int valueColumn
         Boolean inputHasHeader
     }
+
     # Based on a script by Szymon Kielbasa/Ioannis Moustakas
     command <<<
         set -e -o pipefail

ncbi.wdl

@@ -19,6 +19,7 @@ task genomeDownload {
         String? executable = "ncbi-genome-download"
         String? preCommand
     }
+
     command {
         set -e -o pipefail
         ~{preCommand}
@@ -79,6 +80,7 @@ task downloadNtFasta{
         String ntDir = libraryPath + "/nt"
         String ntFilePath = ntDir + "/nt.fna"
     }
+
     command {
         set -e -o pipefail
         mkdir -p ~{ntDir}
@@ -105,6 +107,7 @@ task downloadAccessionToTaxId {
         String downloadDir
         Boolean gzip = false
     }
+
     command {
         set -e -o pipefail
         mkdir -p ~{downloadDir}

picard.wdl

@@ -27,6 +27,7 @@ task CollectMultipleMetrics {
         Float? memory
         Float? memoryMultiplier
     }
+
     Int mem = ceil(select_first([memory, 4.0]))
 
     String toolCommand = if defined(picardJar)
@@ -94,6 +95,7 @@ task CollectRnaSeqMetrics {
         Float? memory
         Float? memoryMultiplier
     }
+
     Int mem = ceil(select_first([memory, 4.0]))
 
     String toolCommand = if defined(picardJar)
@@ -231,8 +233,8 @@ task MarkDuplicates {
         # Sometimes we wish to supply "null" in order to turn off optical duplicate detection
         # This can be desirable if you don't mind the estimated library size being wrong and optical duplicate detection is taking >7 days and failing
         String? read_name_regex
-
     }
+
     # 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"
@@ -283,6 +285,7 @@ task MergeVCFs {
         Float? memory
         Float? memoryMultiplier
     }
+
     # 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]))
@@ -321,6 +324,7 @@ task SamToFastq {
         Float? memory
         Float? memoryMultiplier
     }
+
     Int mem = ceil(select_first([memory, 16.0])) # High memory default to avoid crashes.
 
     String toolCommand = if defined(picardJar)
@@ -359,6 +363,7 @@ task ScatterIntervalList {
         Float? memory
         Float? memoryMultiplier
     }
+
     Int mem = ceil(select_first([memory, 4.0]))
 
     String toolCommand = if defined(picardJar)

samtools.wdl

@@ -6,6 +6,7 @@ task Index {
         File bamFilePath
         String? bamIndexPath
     }
+
     command {
         set -e -o pipefail
         ~{preCommand}
@@ -23,6 +24,7 @@ task Merge {
         Array[File]+ bamFiles
         String outputBamPath
     }
+
     command {
         set -e -o pipefail
         ~{preCommand}
@@ -104,15 +106,18 @@ task fastq {
         ~{"--threads " + totalThreads} \
         ~{inputBam}
     }
+
     output {
         File read1 = outputRead1
         File? read2 = outputRead2
         File? read0 = outputRead0
     }
+
     runtime {
         cpu: totalThreads
         memory: select_first([memory, 1])
     }
+
     parameter_meta {
         preCommand: "A command that is run before the task. Can be used to activate environments"
         inputBam: "The bam file to process."

seqtk.wdl

@@ -13,17 +13,18 @@ task sample {
     }
 
     command {
-    set -e -o pipefail
-    ~{'mkdir -p $(dirname ' + outFilePath + ')'}
-    ~{preCommand}
-    seqtk sample \
-    ~{"-s " + seed} \
-    ~{true="-2 " false="" twoPassMode} \
-    ~{sequenceFile} \
-    ~{number} ~{fraction} \
-    ~{true="| gzip" false="" zip} \
-    ~{"> " + outFilePath}
+        set -e -o pipefail
+        ~{'mkdir -p $(dirname ' + outFilePath + ')'}
+        ~{preCommand}
+        seqtk sample \
+        ~{"-s " + seed} \
+        ~{true="-2 " false="" twoPassMode} \
+        ~{sequenceFile} \
+        ~{number} ~{fraction} \
+        ~{true="| gzip" false="" zip} \
+        ~{"> " + outFilePath}
     }
+
     output {
         File subsampledReads= select_first([outFilePath])
     }

spades.wdl

@@ -31,6 +31,7 @@ task spades {
         Float? covCutoff
         Int? phredOffset
     }
+
     Int finalThreads = select_first([threads])
     Float totalMemory = select_first([memoryGb, finalThreads * 16.0])
     Int finalMemory = ceil(totalMemory)
@@ -67,6 +68,7 @@ task spades {
         ~{"--cov-cutoff " + covCutoff } \
         ~{"--phred-offset " + phredOffset }
     }
+
     output {
         Array[File] correctedReads = glob(outputDir + "/corrected/*.fastq*")
         File scaffolds = outputDir + "/scaffolds.fasta"
@@ -78,6 +80,7 @@ task spades {
         File params = outputDir + "/params.txt"
         File log = outputDir + "/spades.log"
     }
+
     runtime {
         cpu: finalThreads
         memory: clusterMemory

star.wdl

@@ -60,6 +60,7 @@ task makeStarRGline {
         String? platform
         String readgroup
     }
+
     command {
         printf '"ID:~{readgroup}" "LB:~{library}" "PL:~{default="ILLUMINA" platform}" "SM:~{sample}"'
     }

unicycler.wdl

@@ -46,6 +46,7 @@ task unicycler {
         String? scores
         String? lowScore
     }
+
     command {
         set -e -o pipefail
         mkdir -p ~{out}
@@ -92,11 +93,13 @@ task unicycler {
         ~{"--scores " + scores } \
         ~{"--low_score " + lowScore }
     }
+
     output {
         File assemblyFasta = out + "/assembly.fasta"
         File assemblyGfa = out + "/assembly.gfa"
         File log = out + "/unicycler.log"
     }
+
     runtime {
         cpu: select_first([threads])
         memory: select_first([memory])