diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala index 2579be01565cbf92d08519dee02e8ae568000c9f..ad6dd527ca3306a52c5708567af6bba82396e85c 100644 --- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala +++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala @@ -129,8 +129,7 @@ trait MultiSampleQScript extends BiopetQScript { ConfigUtils.any2map(Config.global.map("samples")).keySet } - /** - * Runs addAndTrackJobs method for each sample */ + /** Runs addAndTrackJobs method for each sample */ final def addSamplesJobs() { for ((sampleId, sample) <- samples) { sample.addAndTrackJobs() diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala new file mode 100644 index 0000000000000000000000000000000000000000..531425b7a50bde7a77d62213561cef91095ecdd9 --- /dev/null +++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala @@ -0,0 +1,38 @@ +package nl.lumc.sasc.biopet.extensions + +import java.io.File + +import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction +import nl.lumc.sasc.biopet.core.config.Configurable +import org.broadinstitute.gatk.utils.commandline.{ Output, Input } + +/** + * Created by pjvan_thof on 1/29/15. + * Versions from the executable are not reliable, this extension is based on md5 '3d033ff8a1f4ea9cb3ede12939561141' from the executable + */ +class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction { + @Input(doc = "Input wig file") + var inputWigFile: File = _ + + @Input(doc = "Input chrom sizes file") + var inputChromSizesFile: File = _ + + @Output(doc = "Output BigWig file") + var outputBigWig: File = _ + + executable = config("exe", default = "wigToBigWig") + + var blockSize: Option[Int] = config("blockSize") + var itemsPerSlot: Option[Int] = config("itemsPerSlot") + var clip: Boolean = config("clip", default = false) + var unc: Boolean = config("unc", default = false) + + def cmdLine = required(executable) + + optional("-blockSize=", blockSize, spaceSeparated = false) + + optional("-itemsPerSlot=", itemsPerSlot, spaceSeparated = false) + + conditional(clip, "-clip") + + conditional(unc, "-unc") + + required(inputWigFile) + + required(inputChromSizesFile) + + required(outputBigWig) +} \ No newline at end of file