Commit 00034b55 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge branch 'fix-cutadapt' into 'develop'

Fixed default value

Fixes #294 

See merge request !347
parents 74cbd401 a83a6a3f
......@@ -85,7 +85,7 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
var trimN: Boolean = config("trim_n", default = false)
var prefix: Option[String] = config("prefix")
var suffix: Option[String] = config("suffix")
var stripSuffix: Set[String] = config("strip_suffix")
var stripSuffix: Set[String] = config("strip_suffix", default = Nil)
var lengthTag: Option[String] = config("length_tag")
/** Colorspace options */
......
......@@ -48,7 +48,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
override def defaultThreads = 3
val seqtk = new SeqtkSeq(root)
var clip: Option[Cutadapt] = None
var clip: Option[Cutadapt] = if (!flexiprep.skipClip) Some(new Cutadapt(root, fastqc)) else None
var trim: Option[Sickle] = None
lazy val outputCommand: BiopetCommandLineFunction = if (compress) {
val gzip = Gzip(root)
......@@ -101,7 +101,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
clip = if (!flexiprep.skipClip) {
val foundAdapters = fastqc.foundAdapters.map(_.seq)
if (foundAdapters.nonEmpty) {
val cutadapt = new Cutadapt(root, fastqc)
val cutadapt = clip.getOrElse(new Cutadapt(root, fastqc))
cutadapt.fastqInput = seqtk.output
cutadapt.fastqOutput = new File(output.getParentFile, input.getName + ".cutadapt.fq")
cutadapt.statsOutput = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.clip.stats")
......
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