Commit a8a816b5 authored by bow's avatar bow
Browse files

Style updates

parent 2db37a64
......@@ -95,7 +95,7 @@ class Gentrap(val root: Configurable) extends QScript
case otherwise => throw new IllegalStateException(otherwise.toString)
})) ++ (ribosomalRefFlat match {
case Some(rbs) => Map("ribosomal_intervals" -> rbs.toString)
case None => Map()
case None => Map()
})
/** Default pipeline config */
......
......@@ -377,7 +377,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
sorter.sortOrder = "coordinate"
sorter.isIntermediate = true
add(sorter)
// merge with mapped file
val mergeSamFile = MergeSamFiles(this, List(tophat.outputAcceptedHits, sorter.output),
tophat.output_dir, "coordinate")
......
......@@ -24,7 +24,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Wrapper for the tophat-recondition.py script.
*
*
* NOTE: we are modifying the input and output to be the BAM files directly so the wrapper works nice with Queue.
*/
class TophatRecondition(val root: Configurable) extends PythonCommandLineFunction {
......@@ -45,6 +45,6 @@ class TophatRecondition(val root: Configurable) extends PythonCommandLineFunctio
require(inputBam != null, "Input must be defined.")
require(outputSam != null, "Output must be defined.")
}
def cmdLine = getPythonCommand + required(inputDir) + required(outputDir)
}
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