Commit 2af2676b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove bigwig from output

parent a93b0bbd
......@@ -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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