Commit 6025ff20 authored by Peter van 't Hof's avatar Peter van 't Hof

Format change

parent 4f99194a
......@@ -16,12 +16,12 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.File
import nl.lumc.sasc.biopet.core.summary.{Summarizable, SummaryQScript}
import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, BiopetFifoPipe, BiopetQScript}
import nl.lumc.sasc.biopet.extensions.{Cat, Gzip, Sickle}
import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetFifoPipe, BiopetQScript }
import nl.lumc.sasc.biopet.extensions.{ Cat, Gzip, Sickle }
import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by pjvan_thof on 9/22/15.
......@@ -123,7 +123,7 @@ class QcCommand(val parent: Configurable, val fastqc: Fastqc, val read: String)
Some(cutadapt)
} else None
case (None, _) => None
case (c, _) => c
case (c, _) => c
}
trim.foreach { t =>
......
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