Adding a QC command

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cutadapt.scala

@@ -63,8 +63,8 @@ class Cutadapt(val root: Configurable) extends BiopetCommandLineFunction with Su
     optional("-M", opt_maximum_length) +
     // input / output
     required(fastq_input) +
-    required("--output", fastq_output) +
-    " > " + required(stats_output)
+    (if (outputAsStsout) "" else required("--output", fastq_output) +
+      " > " + required(stats_output))
 
   /** Output summary stats */
   def summaryStats: Map[String, Any] = {

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/Sickle.scala

@@ -48,8 +48,6 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
   @Output(doc = "stats output")
   var output_stats: File = _
 
-  var fastqc: Fastqc = _
-
   executable = config("exe", default = "sickle", freeVar = false)
   var qualityType: Option[String] = config("qualitytype")
   var qualityThreshold: Option[Int] = config("qualityThreshold")
@@ -76,15 +74,15 @@ class Sickle(val root: Configurable) extends BiopetCommandLineFunction with Summ
         required("-s", output_singles)
     } else cmd += required("se")
     cmd +
-      required("-f", input_R1) +
+      (if (inputAsStdin) required("-f", new File("/dev/stdin")) else required("-f", input_R1)) +
       required("-t", qualityType) +
-      required("-o", output_R1) +
+      (if (outputAsStsout) required("-o", new File("/dev/stdout")) else required("-o", output_R1)) +
       optional("-q", qualityThreshold) +
       optional("-l", lengthThreshold) +
       conditional(noFiveprime, "-x") +
       conditional(discardN, "-n") +
-      conditional(quiet, "--quiet") +
-      " > " + required(output_stats)
+      conditional(quiet || outputAsStsout, "--quiet") +
+      (if (outputAsStsout) "" else " > " + required(output_stats))
   }
 
   /** returns stats map for summary */

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

+package nl.lumc.sasc.biopet.pipelines.flexiprep
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, BiopetPipe }
+import nl.lumc.sasc.biopet.extensions.{ Gzip, Zcat, Sickle }
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by pjvan_thof on 9/22/15.
+ */
+class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetCommandLineFunction {
+
+  val flexiprep = root match {
+    case f: Flexiprep => f
+    case _            => throw new IllegalArgumentException("This class may only be used inside Flexiprep")
+  }
+
+  @Input(required = true)
+  var input: File = _
+
+  @Output(required = true)
+  var output: File = _
+
+  val zcat = new Zcat(root)
+  val seqtk = new SeqtkSeq(root)
+  val cutadept = flexiprep.skipClip match {
+    case false => Some(new Cutadapt(root))
+    case true  => None
+  }
+  val sickle = flexiprep.skipTrim match {
+    case false => Some(new Sickle(root))
+    case true  => None
+  }
+  val gzip = Gzip(root)
+
+  override def beforeGraph(): Unit = {
+    super.beforeGraph()
+    deps :::= fastqc.outputFiles
+  }
+
+  override def beforeCmd(): Unit = {
+    seqtk.Q = fastqc.encoding match {
+      case null => None
+      case enc if enc.contains("Sanger / Illumina 1.9") => None
+      case enc if enc.contains("Illumina <1.3") => Option(64)
+      case enc if enc.contains("Illumina 1.3") => Option(64)
+      case enc if enc.contains("Illumina 1.5") => Option(64)
+      case _ => None
+    }
+    if (seqtk.Q.isDefined) seqtk.V = true
+  }
+
+  def cmdLine = {
+    val sanger = seqtk.Q match {
+      case Some(_) => Some(seqtk)
+      case _       => None
+    }
+    val clip = cutadept match {
+      case Some(cutadept) =>
+        val foundAdapters = fastqc.foundAdapters.map(_.seq)
+        if (cutadept.default_clip_mode == "3") cutadept.opt_adapter ++= foundAdapters
+        else if (cutadept.default_clip_mode == "5") cutadept.opt_front ++= foundAdapters
+        else if (cutadept.default_clip_mode == "both") cutadept.opt_anywhere ++= foundAdapters
+        if (foundAdapters.nonEmpty) Some(cutadept)
+        else None
+      case _ => None
+    }
+    val trim = sickle
+    val cmds = ((if (input.getName.endsWith(".gz") || input.getName.endsWith(".gzip")) Some(zcat) else None) ::
+      sanger :: clip :: trim :: Some(gzip) :: Nil).flatten
+    val cmd = input :<: cmds.tail.foldLeft(cmds.head)((a, b) => a | b) > output
+    cmd.beforeGraph()
+    cmd.commandLine
+  }
+}