Commit 89753299 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added flexiprep

parent 790eb131
...@@ -38,6 +38,11 @@ ...@@ -38,6 +38,11 @@
<artifactId>BiopetCore</artifactId> <artifactId>BiopetCore</artifactId>
<version>${project.version}</version> <version>${project.version}</version>
</dependency> </dependency>
<dependency>
<groupId>nl.lumc.sasc</groupId>
<artifactId>Flexiprep</artifactId>
<version>${project.version}</version>
</dependency>
<dependency> <dependency>
<groupId>nl.lumc.sasc</groupId> <groupId>nl.lumc.sasc</groupId>
<artifactId>BiopetToolsExtensions</artifactId> <artifactId>BiopetToolsExtensions</artifactId>
......
...@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript ...@@ -19,6 +19,7 @@ import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile import nl.lumc.sasc.biopet.core.BiopetQScript.InputFile
import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag } import nl.lumc.sasc.biopet.core.{ PipelineCommand, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq import nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript import org.broadinstitute.gatk.queue.QScript
...@@ -88,14 +89,21 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi ...@@ -88,14 +89,21 @@ class GearsSingle(val root: Configurable) extends QScript with SummaryQScript wi
case _ => throw new IllegalArgumentException("Missing input files") case _ => throw new IllegalArgumentException("Missing input files")
} }
lazy val fastaR1 = fastqToFasta(r1, outputName + ".R1") val flexiprep = new Flexiprep(this)
lazy val fastaR2 = r2.map(fastqToFasta(_, outputName + ".R2")) flexiprep.input_R1 = r1
flexiprep.input_R2 = r2
flexiprep.init()
flexiprep.biopetScript()
addAll(flexiprep.functions)
lazy val fastaR1 = fastqToFasta(flexiprep.fastqR1Qc, outputName + ".R1")
lazy val fastaR2 = flexiprep.fastqR2Qc.map(fastqToFasta(_, outputName + ".R2"))
if (gearsUseKraken) { if (gearsUseKraken) {
val kraken = new GearsKraken(this) val kraken = new GearsKraken(this)
kraken.outputDir = new File(outputDir, "kraken") kraken.outputDir = new File(outputDir, "kraken")
kraken.fastqR1 = r1 kraken.fastqR1 = flexiprep.fastqR1Qc
kraken.fastqR2 = r2 kraken.fastqR2 = flexiprep.fastqR2Qc
kraken.outputName = outputName kraken.outputName = outputName
kraken.init() kraken.init()
kraken.biopetScript() kraken.biopetScript()
......
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