Added option to skip abort step

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

@@ -120,10 +120,12 @@ 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 (config("abort_on_corrupt_fastq", default = true)) {
+      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/"))
@@ -271,10 +273,12 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     validateFastq.jobOutputFile = new File(outputDir, ".validate_fastq.qc.log.out")
     add(validateFastq)
 
-    val checkValidateFastq = new CheckValidateFastq
-    checkValidateFastq.inputLogFile = validateFastq.jobOutputFile
-    checkValidateFastq.jobOutputFile = new File(outputDir, ".check.validate_fastq.qc.log.out")
-    add(checkValidateFastq)
+    if (config("abort_on_corrupt_fastq", default = true)) {
+      val checkValidateFastq = new CheckValidateFastq
+      checkValidateFastq.inputLogFile = validateFastq.jobOutputFile
+      checkValidateFastq.jobOutputFile = new File(outputDir, ".check.validate_fastq.qc.log.out")
+      add(checkValidateFastq)
+    }
 
     outputFiles += ("output_R1_gzip" -> fastqR1Qc)
     if (paired) outputFiles += ("output_R2_gzip" -> fastqR2Qc.get)