Commit 52928227 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix code style warnings

parent 699c7baf
......@@ -15,11 +15,9 @@
*/
package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.{ Pbzip2, Zcat, Gzip, Sickle }
import nl.lumc.sasc.biopet.extensions.{ Zcat, Gzip }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, FastqSync }
import org.broadinstitute.gatk.queue.QScript
......@@ -109,7 +107,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
def biopetScript() {
runInitialJobs()
val out = if (paired) runTrimClip(input_R1, input_R2, outputDir)
if (paired) runTrimClip(input_R1, input_R2, outputDir)
else runTrimClip(input_R1, outputDir)
val R1_files = for ((k, v) <- outputFiles if k.endsWith("output_R1")) yield v
......
......@@ -19,7 +19,6 @@ import java.io.File
import java.util.Date
import nl.lumc.sasc.biopet.core._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsSort
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
......@@ -178,13 +177,12 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
var fastq_R2_output: List[File] = Nil
val chunks: Map[File, (File, Option[File])] = {
if (chunking) {
(for (t <- 1 to numberChunks.getOrElse(1)) yield {
if (chunking) (for (t <- 1 to numberChunks.getOrElse(1)) yield {
val chunkDir = new File(outputDir, "chunks" + File.separator + t)
chunkDir -> (new File(chunkDir, input_R1.getName),
if (paired) Some(new File(chunkDir, input_R2.get.getName)) else None)
}).toMap
} else if (skipFlexiprep) Map(outputDir -> (input_R1, (if (paired) input_R2 else None)))
else if (skipFlexiprep) Map(outputDir -> (input_R1, if (paired) input_R2 else None))
else Map(outputDir -> (flexiprep.input_R1, flexiprep.input_R2))
}
......
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