Commit c82dc34f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Code style

parent 29923378
......@@ -95,7 +95,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
sickle.output_stats = new File(flexiprep.outputDir, s"${flexiprep.sampleId.getOrElse("x")}-${flexiprep.libId.getOrElse("x")}.$read.trim.stats")
sickle.input_R1 = clip match {
case Some(c) => c.fastq_output
case _ => seqtk.output
case _ => seqtk.output
}
sickle.output_R1 = new File(output.getParentFile, input.getName + ".sickle.fq")
addPipeJob(sickle)
......@@ -105,7 +105,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
val outputFile = (clip, trim) match {
case (_, Some(t)) => t.output_R1
case (Some(c), _) => c.fastq_output
case _ => seqtk.output
case _ => seqtk.output
}
if (compress) outputCommand = {
......@@ -135,9 +135,9 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
val cmd = (clip, trim) match {
case (Some(c), Some(t)) => new BiopetFifoPipe(root, seqtk :: c :: t :: outputCommand :: Nil)
case (Some(c), _) => new BiopetFifoPipe(root, seqtk :: c :: outputCommand :: Nil)
case (_, Some(t)) => new BiopetFifoPipe(root, seqtk :: t :: outputCommand :: Nil)
case _ => new BiopetFifoPipe(root, seqtk :: outputCommand :: Nil)
case (Some(c), _) => new BiopetFifoPipe(root, seqtk :: c :: outputCommand :: Nil)
case (_, Some(t)) => new BiopetFifoPipe(root, seqtk :: t :: outputCommand :: Nil)
case _ => new BiopetFifoPipe(root, seqtk :: outputCommand :: Nil)
}
//val cmds = (Some(seqtk) :: clip :: trim :: Some(new Gzip(root)) :: Nil).flatten
......
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