Added check abort step in pipeline

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

@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class ValidateFastq(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.ValidateFastq

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

@@ -96,10 +96,10 @@ object ValidateFastq extends ToolCommand {
   private var maxQual: Option[Char] = None
 
   /**
-    *
-    * @param record
-    * @throws IllegalStateException
-    */
+   *
+   * @param record
+   * @throws IllegalStateException
+   */
   private[tools] def checkQualEncoding(record: FastqRecord): Unit = {
     val min = record.getBaseQualityString.min
     val max = record.getBaseQualityString.max
@@ -114,10 +114,10 @@ object ValidateFastq extends ToolCommand {
   }
 
   /**
-    *
-    * @return
-    * @throws IllegalStateException
-    */
+   *
+   * @return
+   * @throws IllegalStateException
+   */
   private[tools] def getPossibleEncodings: List[String] = {
     val buffer: ListBuffer[String] = ListBuffer()
     (minQual, maxQual) match {

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/CheckValidateFastq.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.pipelines.flexiprep
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.summary.WriteSummary
+import org.broadinstitute.gatk.queue.function.InProcessFunction
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input }
+
+import scala.io.Source
+
+/**
+ * This class checks md5sums and give an exit code 1 when md5sum is not the same
+ *
+ * Created by pjvanthof on 16/08/15.
+ */
+class CheckValidateFastq extends InProcessFunction {
+  @Input(required = true)
+  var inputLogFile: File = _
+
+  /** Exits whenever the input md5sum is not the same as the output md5sum */
+  def run: Unit = {
+
+    val reader = Source.fromFile(inputLogFile)
+    reader.getLines().foreach { line =>
+      if (line.startsWith("ERROR")) {
+        logger.error("Corrupt fastq file found, aborting pipeline")
+
+        // 130 Simulates a ctr-C
+        Runtime.getRuntime.halt(130)
+      }
+    }
+    reader.close()
+  }
+}
\ No newline at end of file

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.{ValidateFastq, SeqStat, FastqSync}
+import nl.lumc.sasc.biopet.extensions.tools.{ ValidateFastq, SeqStat, FastqSync }
 
 import org.broadinstitute.gatk.queue.QScript
 
@@ -120,6 +120,11 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     validateFastq.jobOutputFile = new File(outputDir, ".validate_fastq.log.out")
     add(validateFastq)
 
+    val checkValidateFastq = new CheckValidateFastq
+    checkValidateFastq.inputLogFile = validateFastq.jobOutputFile
+    checkValidateFastq.jobOutputFile = new File(outputDir, ".check.validate_fastq.log.out")
+    add(checkValidateFastq)
+
     if (paired) {
       fastqc_R2 = Fastqc(this, input_R2.get, new File(outputDir, R2_name + ".fastqc/"))
       add(fastqc_R2)