From edc5fc7f287da0a5d7bf2f415936358a6e1d4d45 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 11 May 2016 10:20:02 +0200
Subject: [PATCH] Style fix
---
.../nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index d258a33f8..81aee7938 100644
--- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
@@ -35,7 +35,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
/** Allow reporting of all found (potentially adapter) sequences in the FastQC */
var sensitiveAdapterSearch: Boolean = config("sensitiveAdapterSearch", default = false)
- var enableRCtrimming: Boolean = config("enableRCtrimming", default=false)
+ var enableRCtrimming: Boolean = config("enableRCtrimming", default = false)
/** Class for storing a single FastQC module result */
protected case class FastQCModule(name: String, status: String, lines: Seq[String])
@@ -189,9 +189,10 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
val fromKnownList: Set[AdapterSequence] = (adapterSet ++ contaminantSet)
.filter(x => foundAdapterNames.exists(_.startsWith(x.name)))
- val fromKnownListRC: Set[AdapterSequence] = if(enableRCtrimming) fromKnownList.map {
+ val fromKnownListRC: Set[AdapterSequence] = if (enableRCtrimming) fromKnownList.map {
x => AdapterSequence(x.name + "_RC", reverseComplement(x.seq))
- } else Set.empty
+ }
+ else Set.empty
// list all sequences found by FastQC
val fastQCFoundSequences: Seq[AdapterSequence] = if (sensitiveAdapterSearch) {
--
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