Piping compliant

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/seqtk/SeqtkSeq.scala

@@ -28,11 +28,11 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 class SeqtkSeq(val root: Configurable) extends Seqtk {
 
   /** input file */
-  @Input(doc = "Input file (FASTQ or FASTA)")
+  @Input(doc = "Input file (FASTQ or FASTA)", required = !inputAsStdin)
   var input: File = _
 
   /** output file */
-  @Output(doc = "Output file")
+  @Output(doc = "Output file", required = !outputAsStsout)
   var output: File = _
 
   /** mask bases with quality lower than INT [0] */
@@ -106,8 +106,8 @@ class SeqtkSeq(val root: Configurable) extends Seqtk {
       conditional(flag1, "-1") +
       conditional(flag2, "-2") +
       conditional(V, "-V") +
-      required(input) +
-      " > " + required(output)
+      (if (inputAsStdin) "" else required(input)) +
+      (if (outputAsStsout) "" else " > " + required(output))
   }
 
   /**

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

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
-import nl.lumc.sasc.biopet.extensions.Ln
+import nl.lumc.sasc.biopet.extensions.{Cat, Ln}
 
 class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq(root) {
   var fastqc: Fastqc = _
@@ -48,13 +48,22 @@ class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.
       analysisName = getClass.getSimpleName
       super.cmdLine
     } else {
-      analysisName = getClass.getSimpleName + "-ln"
-      Ln(this, input, output).cmd
+      analysisName = getClass.getSimpleName + "-skip"
+      (inputAsStdin, outputAsStsout) match {
+        case (true, true) => super.cmdLine
+        case _ => Ln(this, input, output).cmd
+      }
     }
   }
 }
 
 object SeqtkSeq {
+  def apply(root: Configurable, fastqc: Fastqc = null): SeqtkSeq = {
+    val seqtkSeq = new SeqtkSeq(root)
+    seqtkSeq.fastqc = fastqc
+    seqtkSeq
+  }
+
   def apply(root: Configurable, input: File, output: File, fastqc: Fastqc = null): SeqtkSeq = {
     val seqtkSeq = new SeqtkSeq(root)
     seqtkSeq.input = input