From ff8bbecb95d4daf8cc9415ecdc1b7ea75ac3e54e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 29 Dec 2015 13:23:15 +0100
Subject: [PATCH] Style changes
---
.../sasc/biopet/pipelines/gears/CombineReads.scala | 14 +++++++-------
.../lumc/sasc/biopet/pipelines/gears/Gears.scala | 6 +++---
.../sasc/biopet/pipelines/gears/GearsKraken.scala | 4 ++--
.../biopet/pipelines/gears/GearsQiimeClosed.scala | 2 +-
.../sasc/biopet/pipelines/gears/GearsReport.scala | 2 +-
.../biopet/pipelines/gears/GearsSeqCount.scala | 6 +++---
6 files changed, 17 insertions(+), 17 deletions(-)
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
index cd14d2323..40b40c141 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/CombineReads.scala
@@ -2,23 +2,23 @@ package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.SampleLibraryTag
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.{Cutadapt, Flash}
+import nl.lumc.sasc.biopet.extensions.{ Cutadapt, Flash }
import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
- * Created by pjvanthof on 29/12/15.
- */
+ * Created by pjvanthof on 29/12/15.
+ */
class CombineReads(val root: Configurable) extends QScript with SummaryQScript with SampleLibraryTag {
@Input(doc = "R1 reads in FastQ format", shortName = "R1", required = false)
var fastqR1: File = _
@Input(doc = "R2 reads in FastQ format", shortName = "R2", required = false)
var fastqR2: File = _
-
+
override def fixedValues = Map("flash" -> Map("compress" -> true))
-
+
/** Init for pipeline */
def init(): Unit = {
}
@@ -27,7 +27,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
private lazy val forwardPrimers: List[String] = config("forward_primers")
private lazy val reversePrimers: List[String] = config("reverse_primers")
-
+
def combinedFastq: File = if ((forwardPrimers :: reversePrimers).nonEmpty)
swapExt(outputDir, flash.combinedFastq, ".fastq.gz", ".clip.fastq.gz")
else flash.combinedFastq
@@ -57,7 +57,7 @@ class CombineReads(val root: Configurable) extends QScript with SummaryQScript w
add(cutadapt)
addSummarizable(cutadapt, "cutadapt")
}
-
+
val combinedFastqc = Fastqc(this, this.combinedFastq, new File(outputDir, "combined_fastqc"))
add(combinedFastqc)
addSummarizable(combinedFastqc, "fastqc_combined")
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
index ac38cb34c..ba29af9d5 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
@@ -156,9 +156,9 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
/** File to put in the summary for thie pipeline */
def summaryFiles: Map[String, File] = (
- qiimeClosedOtuTable.map("qiime_closed_otu_table" -> _) ++
- qiimeClosedOtuMap.map("qiime_closed_otu_map" -> _)
- ).toMap
+ qiimeClosedOtuTable.map("qiime_closed_otu_table" -> _) ++
+ qiimeClosedOtuMap.map("qiime_closed_otu_map" -> _)
+ ).toMap
}
object Gears extends PipelineCommand
\ No newline at end of file
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
index 3c7b0d0f5..d1eda0174 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsKraken.scala
@@ -127,11 +127,11 @@ object GearsKraken {
if (k == "root") {
val unclassified = summaries(sample)("unclassified").asInstanceOf[Map[String, Any]]("size").asInstanceOf[Long]
<val>
- {getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0).toString.toLong + unclassified}
+ { getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0).toString.toLong + unclassified }
</val>
} else {
<val>
- {getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0)}
+ { getValue(sample, (path ::: k :: Nil).tail, "size").getOrElse(0) }
</val>
}
}
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
index f78a7f207..cad365753 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala
@@ -59,7 +59,7 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
def summarySettings: Map[String, Any] = Map()
/** File to put in the summary for thie pipeline */
- def summaryFiles: Map[String, File] = Map("otu_table" -> otuTable,"otu_map" -> otuMap)
+ def summaryFiles: Map[String, File] = Map("otu_table" -> otuTable, "otu_map" -> otuMap)
/** Name of summary output file */
def summaryFile: File = new File(outputDir, "summary.closed_reference.json")
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
index 8c8dcc6a8..aa819f08c 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
@@ -80,7 +80,7 @@ object GearsReport extends MultisampleReportBuilder {
ReportPage(
(if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
- ) ::: (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
+ ) ::: (if (krakenExecuted) List("Kraken" -> ReportPage(List(), List(
"Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> ReportPage(List(), List(
diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala
index 94968849c..70b850ce1 100644
--- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala
+++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSeqCount.scala
@@ -1,14 +1,14 @@
package nl.lumc.sasc.biopet.pipelines.gears
-import nl.lumc.sasc.biopet.core.{BiopetQScript, SampleLibraryTag}
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, SampleLibraryTag }
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.tools.SageCountFastq
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
/**
- * Created by pjvan_thof on 12/29/15.
- */
+ * Created by pjvan_thof on 12/29/15.
+ */
class GearsSeqCount(val root: Configurable) extends QScript with BiopetQScript with SampleLibraryTag {
var fastqInput: File = _
--
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