Commit 7bea64ef authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added bwa aln extension

parent 36e763df
package nl.lumc.sasc.biopet.extensions.bwa
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
* Created by pjvan_thof on 1/16/15.
*/
class BwaAln(val root: Configurable) extends Bwa {
@Input(doc = "Fastq file", required = true)
var fastq: File = _
@Input(doc = "The reference file for the bam files.", required = true)
var reference: File = config("reference", required = true)
@Output(doc = "Output file SAM", required = false)
var output: File = _
var n: Option[Int] = config("n")
var o: Option[Int] = config("o")
var e: Option[Int] = config("e")
var i: Option[Int] = config("i")
var d: Option[Int] = config("d")
var l: Option[Int] = config("l")
var k: Option[Int] = config("k")
var m: Option[Int] = config("m")
var M: Option[Int] = config("M")
var O: Option[Int] = config("O")
var E: Option[Int] = config("E")
var R: Option[Int] = config("R")
var q: Option[Int] = config("q")
var B: Option[Int] = config("B")
var L: Boolean = config("L", default = false)
var N: Boolean = config("N", default = false)
var I: Boolean = config("I", default = false)
var b: Boolean = config("b", default = false)
var n0: Boolean = config("0", default = false)
var n1: Boolean = config("1", default = false)
var n2: Boolean = config("2", default = false)
var Y: Boolean = config("Y", default = false)
override val defaultVmem = "5G"
override val defaultThreads = 8
def cmdLine = required(executable) +
required("aln") +
optional("-n", n) +
optional("-o", o) +
optional("-e", e) +
optional("-i", i) +
optional("-d", d) +
optional("-l", l) +
optional("-k", k) +
optional("-m", m) +
optional("-M", M) +
optional("-O", O) +
optional("-E", E) +
optional("-R", R) +
optional("-q", q) +
optional("-B", B) +
conditional(L, "-L") +
conditional(N, "-N") +
conditional(I, "-I") +
conditional(b, "-b") +
conditional(n0, "-0") +
conditional(n1, "-1") +
conditional(n2, "-2") +
conditional(Y, "-Y") +
required("-f", output) +
required(reference) +
required(fastq)
}
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