Add initial gentrap main interface

gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

+/**
+ * Copyright (c) 2014 Leiden University Medical Center
+ *
+ * @author Wibowo Arindrarto
+ */
+
 package nl.lumc.sasc.biopet.pipelines.gentrap
 
 import org.broadinstitute.gatk.queue.QScript
@@ -10,10 +16,60 @@ import nl.lumc.sasc.biopet.core.config._
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 import nl.lumc.sasc.biopet.pipelines.mapping.Mapping
 
+/**
+ * Gentrap pipeline
+ * Generic transcriptome analysis pipeline
+ */
 class Gentrap(val root: Configurable) extends QScript with BiopetQScript {
+
   def this() = this(null)
 
+  /** Read 1 input */
+  @Input(doc = "FASTQ file input (single-end or pair 1)", fullName = "input_r1", shortName = "R1", required = true)
+  var inputR1: File = _
+
+  /** Read 2 input (optional) */
+  @Input(doc = "FASTQ file input (pair 2)", fullName = "input_r2", shortName = "R2", required = false)
+  var inputR2: File = _
+
+  /** Split aligner to use */
+  @Argument(doc = "Split aligner", fullName = "aligner", shortName = "aln", required = true, validation = "gsnap|tophat|star")
+  var aligner: String = _
+
+  /** Whether library is strand-specifc (dUTP protocol) or not */
+  @Argument(doc = "Whether input data was made using the dUTP strand-specific protocol", fullName = "strand_specific", shortName = "strandSpec", required = true)
+  var strandSpec: Boolean = _
+
+  /** Variant calling */
+  @Argument(doc = "Variant caller", fullName = "variant_caller", shortName = "varCaller", required = false, validation = "varscan|snvmix")
+  var varcaller: String = _
+
+  /** Cufflinks assembly type */
+  @Argument(doc = "Cufflinks assembly type", fullName = "transcript_asm", shortName = "transAsm", required = false, validation = "none|strict|guided|blind")
+  var asm: List[String] = List("none")
+
+  /** FASTQ trimming */
+  @Argument(doc = "Whether to skip trimming input files", fullName = "skip_trim_input", shortName = "skipTrim", required = false)
+  var skipTrim: Boolean = false
+
+  /** FASTQ clipping */
+  @Argument(doc = "Whether to skip clipping input files", fullName = "skip_clip_input", shortName = "skipClip", required = false)
+  var skipClip: Boolean = false
+
+  /** Gene-wise read count table output */
+  @Argument(doc = "Gene read count table output", fullName = "count_gene_read", shortName = "cGeneRead", required = false)
+  var cGeneRead: Boolean = _
+
+  /** Gene-wise base count table output */
+  @Argument(doc = "Gene base count table output", fullName = "count_gene_base", shortName = "cGeneBase", required = false)
+  var cGeneBase: Boolean = _
+
+  /** Exon-wise base count table output */
+  @Argument(doc = "Exon base count table output", fullName = "count_exon_base", shortName = "cExonBase", required = false)
+  var cExonBase: Boolean = _
+
   def init() {
+    for (file <- configfiles) globalConfig.loadConfigFile(file)
   }
 
   def biopetScript() {