From 48b7822fc2f93e8f6599c0e4c5566fdf2b5f7eaa Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 16 Mar 2016 16:50:25 +0100
Subject: [PATCH] Added wigle and tdf files to summary
---
.../biopet/pipelines/bamtobigwig/Bam2Wig.scala | 10 +++++++---
.../sasc/biopet/pipelines/mapping/Mapping.scala | 16 +++++++++++++---
2 files changed, 20 insertions(+), 6 deletions(-)
diff --git a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
index fb9e39611..4e65a7f59 100644
--- a/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+++ b/public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
@@ -38,6 +38,10 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
inputFiles :+= new InputFile(bamFile)
}
+ def outputWigleFile = new File(outputDir, bamFile.getName + ".wig")
+ def outputTdfFile = new File(outputDir, bamFile.getName + ".tdf")
+ def outputBwFile = new File(outputDir, bamFile.getName + ".bw")
+
def biopetScript(): Unit = {
val bs = new BamToChromSizes(this)
bs.bamFile = bamFile
@@ -48,14 +52,14 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
val igvCount = new IGVToolsCount(this)
igvCount.input = bamFile
igvCount.genomeChromSizes = bs.chromSizesFile
- igvCount.wig = Some(new File(outputDir, bamFile.getName + ".wig"))
- igvCount.tdf = Some(new File(outputDir, bamFile.getName + ".tdf"))
+ igvCount.wig = Some(outputWigleFile)
+ igvCount.tdf = Some(outputTdfFile)
add(igvCount)
val wigToBigWig = new WigToBigWig(this)
wigToBigWig.inputWigFile = igvCount.wig.get
wigToBigWig.inputChromSizesFile = bs.chromSizesFile
- wigToBigWig.outputBigWig = new File(outputDir, bamFile.getName + ".bw")
+ wigToBigWig.outputBigWig = outputBwFile
add(wigToBigWig)
}
}
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index fa1494e6c..47532b329 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -109,7 +109,14 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** File to add to the summary */
def summaryFiles: Map[String, File] = Map("output_bam" -> finalBamFile, "input_R1" -> inputR1,
"reference" -> referenceFasta()) ++
- (if (inputR2.isDefined) Map("input_R2" -> inputR2.get) else Map())
+ (if (inputR2.isDefined) Map("input_R2" -> inputR2.get) else Map()) ++
+ (bam2wig match {
+ case Some(b) => Map(
+ "output_wigle" -> b.outputWigleFile,
+ "output_tdf" -> b.outputTdfFile,
+ "output_bigwig" -> b.outputBwFile)
+ case _ => Map()
+ })
/** Settings to add to summary */
def summarySettings = Map(
@@ -270,12 +277,15 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
add(gears)
}
- if (config("generate_wig", default = false).asBoolean)
- addAll(Bam2Wig(this, finalBamFile).functions)
+ bam2wig.foreach(add(_))
addSummaryJobs()
}
+ protected lazy val bam2wig = if (config("generate_wig", default = false)) {
+ Some(Bam2Wig(this, finalBamFile))
+ } else None
+
/** Add bwa aln jobs */
def addBwaAln(R1: File, R2: Option[File], output: File): File = {
val bwaAlnR1 = new BwaAln(this)
--
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