Add cutadapt statistics output to flexiprep runs

flexiprep/src/main/scala/nl/lumc/sasc/biopet/function/fastq/Cutadapt.scala

@@ -19,6 +19,9 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
   @Output(doc = "Output fastq file")
   var fastq_output: File = _
 
+  @Output(doc = "Output statistics file")
+  var stats_output: File = _
+
   executable = config("exe", default = "cutadapt")
   override def versionCommand = executable + " --version"
   override val versionRegex = """(.*)""".r
@@ -49,7 +52,8 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction {
         optional("-M", opt_maximum_length) +
         // input / output
         required(fastq_input) +
-        " > " + required(fastq_output)
+        required("--output", fastq_output) +
+        " > " + required(stats_output)
     } else {
       analysisName = getClass.getSimpleName + "-ln"
       "ln -sf " +

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

@@ -128,13 +128,19 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
     var R2: File = new File(R2_in)
 
     if (!skipClip) { // Adapter clipping
+
       val cutadapt_R1 = new Cutadapt(this)
+
       if (!skipTrim || paired) cutadapt_R1.isIntermediate = true
       cutadapt_R1.fastq_input = R1
       cutadapt_R1.fastq_output = swapExt(outDir, R1, R1_ext, ".clip" + R1_ext)
+      cutadapt_R1.stats_output = swapExt(outDir, R1, R1_ext, ".clip.stats")
+
       if (outputFiles.contains("contams_R1")) cutadapt_R1.contams_file = outputFiles("contams_R1")
+
       add(cutadapt_R1)
       R1 = cutadapt_R1.fastq_output
+
       if (paired) {
         val cutadapt_R2 = new Cutadapt(this)
         if (!skipTrim || paired) cutadapt_R2.isIntermediate = true