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Commit 0dc6aa4c authored by Peter van 't Hof's avatar Peter van 't Hof
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parent 884091eb
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Showing with 4 additions and 4 deletions
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSample.scala
View file @ 0dc6aa4c
......@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.seqtk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Wrapper for the seqtk sample subcommand.
......@@ -41,7 +41,7 @@ class SeqtkSample(val root: Configurable) extends Seqtk {
" sample " +
optional("-s", s) +
required(input) +
(if (sample > 1) required(sample.toInt) else required(sample) ) +
(if (sample > 1) required(sample.toInt) else required(sample)) +
(if (outputAsStsout) "" else " > " + required(output))
}
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @ 0dc6aa4c
......@@ -15,9 +15,9 @@
package nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import nl.lumc.sasc.biopet.core.{MultiSampleQScript, PipelineCommand}
import nl.lumc.sasc.biopet.core.{ MultiSampleQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.tools.MergeOtuMaps
import nl.lumc.sasc.biopet.extensions.{Bgzip, Gzip, Ln, Zcat}
import nl.lumc.sasc.biopet.extensions.{ Bgzip, Gzip, Ln, Zcat }
import nl.lumc.sasc.biopet.extensions.qiime.MergeOtuTables
import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSample
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
......
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