Commit a83a6a3f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed the cutadapt so the config will always load, even when fastqc data is no yet avilable

parent 6dda3f45
......@@ -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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