Commit 43100197 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Style fixes

parent 08070144
package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.{ PipelineCommand, MultiSampleQScript }
import nl.lumc.sasc.biopet.extensions.{Gzip, Zcat, Ln}
import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat, Ln }
import nl.lumc.sasc.biopet.extensions.qiime.{ MergeOtuMaps, MergeOtuTables }
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.utils.config.Configurable
......@@ -127,10 +127,7 @@ class Gears(val root: Configurable) extends QScript with MultiSampleQScript { qs
val mergeR1: File = new File(sampleDir, s"$sampleId.R1.fq.gz")
add(Zcat(qscript, flexipreps.map(_.fastqR1Qc)) | new Gzip(qscript) > mergeR1)
val mergeR2 = if (flexipreps.exists(_.paired)) {
Some(new File(sampleDir, s"$sampleId.R2.fq.gz"))
} else None
val mergeR2 = if (flexipreps.exists(_.paired)) Some(new File(sampleDir, s"$sampleId.R2.fq.gz")) else None
mergeR2.foreach { file =>
add(Zcat(qscript, flexipreps.flatMap(_.fastqR2Qc)) | new Gzip(qscript) > file)
}
......
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