Commit a4553c54 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed compile issues

parent 912d98fe
......@@ -59,7 +59,7 @@ class Centrifuge(val root: Configurable) extends BiopetCommandLineFunction with
var norc: Boolean = config("norc", default = false)
// Classification args
var minHitlen = Option[Int] = config("min_hitlen")
var minHitlen: Option[Int] = config("min_hitlen")
var minTotallen: Option[Int] = config("min_totallen")
var hostTaxids: List[Int] = config("host_taxids", default = Nil)
var excludeTaxids: List[Int] = config("exclude_taxids", default = Nil)
......
......@@ -163,8 +163,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
gs.libId = Some(libId)
gs.outputDir = libDir
gs.fastqR1 = Some(addDownsample(flexiprep.fastqR1Qc, gs.outputDir))
gs.fastqR2 = flexiprep.fastqR2Qc.map(addDownsample(_, gs.outputDir))
gs.fastqR1 = List(addDownsample(flexiprep.fastqR1Qc, gs.outputDir))
gs.fastqR2 = flexiprep.fastqR2Qc.map(addDownsample(_, gs.outputDir)).toList
add(gs)
}
}
......@@ -194,8 +194,8 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
add(Zcat(qscript, flexipreps.flatMap(_.fastqR2Qc)) | new Gzip(qscript) > file)
}
gearsSingle.fastqR1 = Some(addDownsample(mergeR1, gearsSingle.outputDir))
gearsSingle.fastqR2 = mergeR2.map(addDownsample(_, gearsSingle.outputDir))
gearsSingle.fastqR1 = List(addDownsample(mergeR1, gearsSingle.outputDir))
gearsSingle.fastqR2 = mergeR2.map(addDownsample(_, gearsSingle.outputDir)).toList
add(gearsSingle)
}
......
......@@ -80,8 +80,8 @@ abstract class TestGearsSingle extends TestNGSuite with Matchers {
inputMode match {
case Some("fastq") =>
gears.fastqR1 = Some(TestGearsSingle.r1)
gears.fastqR2 = if (paired) Some(TestGearsSingle.r2) else None
gears.fastqR1 = List(TestGearsSingle.r1)
gears.fastqR2 = if (paired) List(TestGearsSingle.r2) else Nil
case Some("bam") => gears.bamFile = Some(TestGearsSingle.bam)
case None =>
case _ => new IllegalStateException(s"$inputMode not allowed as inputMode")
......
......@@ -219,8 +219,8 @@ trait MultisampleMappingTrait extends MultiSampleQScript
def keepMergedFiles: Boolean = config("keep_merged_files", default = true)
/**
* @deprecated
*/
* @deprecated
*/
lazy val unmappedToGears: Boolean = config("unmapped_to_gears", default = false)
if (config.contains("unmapped_to_gears")) logger.warn("Config value 'unmapped_to_gears' is replaced with 'mapping_to_gears', Assumes default: mapping_to_gears=unmapped")
......@@ -272,7 +272,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
gears.outputDir = new File(sampleDir, "gears")
add(gears)
case "none" =>
case x => Logging.addError(s"${x} is not a valid value for 'mapping_to_gears'")
case x => Logging.addError(s"${x} is not a valid value for 'mapping_to_gears'")
}
}
}
......
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