Commit 3e4e6bad authored by bow's avatar bow
Browse files

Merge branch 'develop' into feature-Chipcap

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
parents a42f82e6 9691531b
......@@ -129,9 +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()
......
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
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment