Commit ee4de907 authored by pjvan_thof's avatar pjvan_thof
Browse files

Style fixes

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