Adding ValidateFastq to flexiprep

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/ValidateFastq.scala

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+
+class ValidateFastq(val root: Configurable) extends ToolCommandFunction {
+  def toolObject = nl.lumc.sasc.biopet.tools.ValidateFastq
+
+  @Input(doc = "Input R1 fastq file", required = true)
+  var r1Fastq: File = _
+
+  @Input(doc = "Input R1 fastq file", required = false)
+  var r2Fastq: Option[File] = None
+
+  override def cmdLine = super.cmdLine +
+    required("-i", r1Fastq) +
+    optional("-j", r2Fastq)
+}

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, SampleLibrary
 import nl.lumc.sasc.biopet.extensions.{ Zcat, Gzip }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.IoUtils._
-import nl.lumc.sasc.biopet.extensions.tools.{ SeqStat, FastqSync }
+import nl.lumc.sasc.biopet.extensions.tools.{ValidateFastq, SeqStat, FastqSync}
 
 import org.broadinstitute.gatk.queue.QScript
 
@@ -114,6 +114,12 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     addSummarizable(fastqc_R1, "fastqc_R1")
     outputFiles += ("fastqc_R1" -> fastqc_R1.output)
 
+    val validateFastq = new ValidateFastq(this)
+    validateFastq.r1Fastq = input_R1
+    validateFastq.r2Fastq = input_R2
+    validateFastq.jobOutputFile = new File(outputDir, ".validate_fastq.log.out")
+    add(validateFastq)
+
     if (paired) {
       fastqc_R2 = Fastqc(this, input_R2.get, new File(outputDir, R2_name + ".fastqc/"))
       add(fastqc_R2)