Commit d03a8edd authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

style changes

parent 857a2b9c
......@@ -2,13 +2,13 @@ package nl.lumc.sasc.biopet.extensions.qiime
import java.io.File
import nl.lumc.sasc.biopet.core.{Version, BiopetCommandLineFunction}
import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by pjvan_thof on 12/10/15.
*/
* Created by pjvan_thof on 12/10/15.
*/
class SplitLibrariesFastq(val root: Configurable) extends BiopetCommandLineFunction with Version {
executable = config("exe", default = "split_libraries_fastq.py")
......@@ -55,7 +55,7 @@ class SplitLibrariesFastq(val root: Configurable) extends BiopetCommandLineFunct
conditional(store_qual_scores, "--store_qual_scores") +
(sample_ids match {
case l: List[_] if l.nonEmpty => optional("--sample_ids", l.mkString(","))
case _ => ""
case _ => ""
}) +
conditional(store_demultiplexed_fastq, "--store_demultiplexed_fastq") +
conditional(retain_unassigned_reads, "--retain_unassigned_reads") +
......
package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.{SampleLibraryTag, BiopetQScript}
import nl.lumc.sasc.biopet.extensions.qiime.{SplitLibrariesFastq, AssignTaxonomy, PickRepSet, PickOtus}
import nl.lumc.sasc.biopet.core.{ SampleLibraryTag, BiopetQScript }
import nl.lumc.sasc.biopet.extensions.qiime.{ SplitLibrariesFastq, AssignTaxonomy, PickRepSet, PickOtus }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
......
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