From c82dc34f0ccc9b4b88ad116428b66152833ffea7 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 15 Oct 2015 13:25:28 +0200
Subject: [PATCH] Code style
---
.../sasc/biopet/pipelines/flexiprep/QcCommand.scala | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
index 9a82541a4..8509b7898 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
@@ -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
--
GitLab