Commit 72896404 authored by Peter van 't Hof's avatar Peter van 't Hof

Style fixes

parent 79b33e3a
......@@ -13,11 +13,10 @@ class WisecondorCount(val root: Configurable) extends Wisecondor {
@Input
var inputBam: File = _
def cmdLine = {
executable + required("count") +
required("-I", inputBam) +
required("-O", output) +
required("-R", referenceFasta()) +
binCommand
}
def cmdLine = executable +
required("count") +
required("-I", inputBam) +
required("-O", output) +
required("-R", referenceFasta()) +
binCommand
}
......@@ -18,16 +18,14 @@ class WisecondorGcCorrect(val root: Configurable) extends Wisecondor {
var nIter: Option[Int] = config("iter", namespace = "wisecondor", default = None)
var fracLowess: Option[Float] = config("frac_lowess", namespace = "wisecondor", default = None)
def cmdLine = {
executable + required("gc-correct") +
required("-I", inputBed) +
required("-R", referenceFasta()) +
required("-O", output) +
binCommand +
optional("-n", fracN) +
optional("-r", fracR) +
optional("-t", nIter) +
optional("-l", fracLowess)
}
def cmdLine = executable +
required("gc-correct") +
required("-I", inputBed) +
required("-R", referenceFasta()) +
required("-O", output) +
binCommand +
optional("-n", fracN) +
optional("-r", fracR) +
optional("-t", nIter) +
optional("-l", fracLowess)
}
......@@ -6,8 +6,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by Sander Bollen on 22-3-17.
*/
* Created by Sander Bollen on 22-3-17.
*/
class WisecondorNewRef(val root: Configurable) extends Wisecondor {
@Input
......@@ -15,13 +15,12 @@ class WisecondorNewRef(val root: Configurable) extends Wisecondor {
var nNeighbourBins: Option[Int] = config("n_neighbour_bins", namespace = "wisecondor", default = None)
def cmdLine = {
executable + required("newref") +
repeat("-I", inputBeds) +
required("-O", output) +
required("-R", referenceFasta()) +
binCommand +
optional("-n", nNeighbourBins)
}
def cmdLine = executable +
required("newref") +
repeat("-I", inputBeds) +
required("-O", output) +
required("-R", referenceFasta()) +
binCommand +
optional("-n", nNeighbourBins)
}
......@@ -16,12 +16,11 @@ class WisecondorZscore(val root: Configurable) extends Wisecondor {
@Input
var referenceDictionary: File = config("reference_dictionary", namespace = "wisecondor")
def cmdLine = {
executable + required("zscore") +
required("-I", inputBed) +
required("-O", output) +
required("-R", referenceFasta()) +
required("-D", referenceDictionary) +
binCommand
}
def cmdLine = executable +
required("zscore") +
required("-I", inputBed) +
required("-O", output) +
required("-R", referenceFasta()) +
required("-D", referenceDictionary) +
binCommand
}
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