Commit ee4de907 authored by pjvan_thof's avatar pjvan_thof

Style fixes

parent 26ff1d93
......@@ -54,7 +54,8 @@ class Stringtie(val parent: Configurable)
/** Regex to get version from version command output */
def versionRegex: Regex = ".*".r
def cmdLine: String = required(executable) +
def cmdLine: String =
required(executable) +
required(inputBam) +
conditional(v, "-v") +
required("-p", threads) +
......
......@@ -39,7 +39,8 @@ class StringtieMerge(val parent: Configurable)
/** Regex to get version from version command output */
def versionRegex: Regex = ".*".r
def cmdLine: String = required(executable) +
def cmdLine: String =
required(executable) +
required("--merge")
conditional(v, "-v") +
required("-p", threads) +
......@@ -53,4 +54,4 @@ class StringtieMerge(val parent: Configurable)
(if (outputAsStdout) "" else required("-o", outputGtf)) +
repeat(inputGtfs)
}
}
......@@ -305,7 +305,8 @@ object Gentrap extends PipelineCommand {
/** Enumeration of available expression measures */
object ExpMeasures extends Enumeration {
val FragmentsPerGene, BaseCounts, CufflinksStrict, CufflinksGuided, CufflinksBlind, Stringtie = Value
val FragmentsPerGene, BaseCounts, CufflinksStrict, CufflinksGuided, CufflinksBlind, Stringtie =
Value
}
/** Enumeration of available strandedness */
......
......@@ -22,10 +22,7 @@ import org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvan_thof on 1/12/16.
*/
class Stringtie(val parent: Configurable)
extends QScript
with Measurement
with AnnotationGtf {
class Stringtie(val parent: Configurable) extends QScript with Measurement with AnnotationGtf {
def mergeArgs = MergeArgs(idCols = List(1), valCol = 2, fallback = "0")
/** Pipeline itself */
......
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