Commit ee4de907 authored by pjvan_thof's avatar pjvan_thof

Style fixes

parent 26ff1d93
...@@ -9,7 +9,7 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output} ...@@ -9,7 +9,7 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import scala.util.matching.Regex import scala.util.matching.Regex
class Stringtie(val parent: Configurable) class Stringtie(val parent: Configurable)
extends BiopetCommandLineFunction extends BiopetCommandLineFunction
with Reference with Reference
with Version { with Version {
...@@ -54,28 +54,29 @@ class Stringtie(val parent: Configurable) ...@@ -54,28 +54,29 @@ 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(inputBam) + required(executable) +
conditional(v, "-v") + required(inputBam) +
required("-p", threads) + conditional(v, "-v") +
conditional(rf, "--rf") + required("-p", threads) +
conditional(fr, "--fr") + conditional(rf, "--rf") +
optional("-l", l) + conditional(fr, "--fr") +
optional("-f", f) + optional("-l", l) +
optional("-m", m) + optional("-f", f) +
optional("-A", geneAbundances) + optional("-m", m) +
optional("-C", referenceCoverage) + optional("-A", geneAbundances) +
optional("-a", a) + optional("-C", referenceCoverage) +
optional("-j", j) + optional("-a", a) +
conditional(t, "-t") + optional("-j", j) +
optional("-c", c) + conditional(t, "-t") +
optional("-g", g) + optional("-c", c) +
conditional(B, "-B") + optional("-g", g) +
optional("-b", b) + conditional(B, "-B") +
conditional(e, "-e") + optional("-b", b) +
optional("-M", M) + conditional(e, "-e") +
optional("-G", referenceGtf) + optional("-M", M) +
(if (x.nonEmpty) optional("-x", x.mkString(",")) else "") + optional("-G", referenceGtf) +
(if (outputAsStdout) "" else required("-o", outputGtf)) (if (x.nonEmpty) optional("-x", x.mkString(",")) else "") +
(if (outputAsStdout) "" else required("-o", outputGtf))
} }
...@@ -9,48 +9,49 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output} ...@@ -9,48 +9,49 @@ import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import scala.util.matching.Regex import scala.util.matching.Regex
class StringtieMerge(val parent: Configurable) class StringtieMerge(val parent: Configurable)
extends BiopetCommandLineFunction extends BiopetCommandLineFunction
with Reference with Reference
with Version { with Version {
executable = config("exe", "stringtie") executable = config("exe", "stringtie")
@Input(required = true) @Input(required = true)
var inputGtfs: List[File] = Nil var inputGtfs: List[File] = Nil
@Input(required = false) @Input(required = false)
var referenceGtf: Option[File] = None var referenceGtf: Option[File] = None
@Output @Output
var outputGtf: File = _ var outputGtf: File = _
var v: Boolean = config("v", default = logger.isDebugEnabled) var v: Boolean = config("v", default = logger.isDebugEnabled)
var l: Option[String] = None var l: Option[String] = None
var f: Option[Double] = config("f") var f: Option[Double] = config("f")
var m: Option[Int] = config("m") var m: Option[Int] = config("m")
var c: Option[Float] = config("c") var c: Option[Float] = config("c")
var F: Option[Double] = config("F") var F: Option[Double] = config("F")
var T: Option[Double] = config("T") var T: Option[Double] = config("T")
var i: Boolean = config("i", default = false) var i: Boolean = config("i", default = false)
/** Command to get version of executable */ /** Command to get version of executable */
def versionCommand: String = executable + " --version" def versionCommand: String = executable + " --version"
/** 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) +
optional("-l", l) + optional("-l", l) +
optional("-f", f) + optional("-f", f) +
optional("-m", m) + optional("-m", m) +
optional("-c", c) + optional("-c", c) +
optional("-F", F) + optional("-F", F) +
conditional(i, "-i") + conditional(i, "-i") +
optional("-G", referenceGtf) + optional("-G", referenceGtf) +
(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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