From 2af2676b26df0358aca4a06da4bbaf7a10d9621a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 6 Feb 2015 19:23:38 +0100
Subject: [PATCH] Remove bigwig from output
---
.../sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala | 10 ++++------
1 file changed, 4 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 159ad4153..9af1eee60 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
@@ -13,19 +13,16 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
- @Input(doc="", required = true)
+ @Input(doc = "Input bam file", required = true)
var bamFile: File = _
- @Output(doc="", required = true)
- var bigWigFile: File = _
-
def init(): Unit = {
}
def biopetScript(): Unit = {
val bs = new BamToChromSizes(this)
bs.bamFile = bamFile
- bs.chromSizesFile = bamFile.getAbsoluteFile + ".chromsizes"
+ bs.chromSizesFile = bamFile.getAbsoluteFile + ".chrom.sizes"
bs.isIntermediate = true
add(bs)
@@ -33,12 +30,13 @@ class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
igvCount.input = bamFile
igvCount.genomeChromSizes = bs.chromSizesFile
igvCount.wig = Some(swapExt(outputDir, bamFile, ".bam", ".wig"))
+ igvCount.tdf = Some(swapExt(outputDir, bamFile, ".bam", ".tdf"))
add(igvCount)
val wigToBigWig = new WigToBigWig(this)
wigToBigWig.inputWigFile = igvCount.wig.get
wigToBigWig.inputChromSizesFile = bs.chromSizesFile
- wigToBigWig.outputBigWig = bigWigFile
+ wigToBigWig.outputBigWig = swapExt(outputDir, bamFile, ".bam", ".bigwig")
add(wigToBigWig)
}
}
--
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