Commit b840a916 authored by bow's avatar bow

Add initial gentrap main interface

parent a90b06da
/**
* 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() {
......
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