Commit 85b9861f authored by bow's avatar bow
Browse files

Merge branch 'patch-bowtie' into 'develop'

Patch bowtie

Fix error on paired end reads for bowtie

See merge request !106
parents 8dd310e6 fd8d9ae0
......@@ -23,16 +23,16 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Fastq file R1", shortName = "R1")
var R1: File = _
var R1: File = null
@Input(doc = "Fastq file R2", shortName = "R2", required = false)
var R2: File = _
var R2: Option[File] = None
@Input(doc = "The reference file for the bam files.", shortName = "R")
@Input(doc = "The reference file for the bam files.", shortName = "R", required = true)
var reference: File = config("reference")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
@Output(doc = "Output file SAM", shortName = "output", required = true)
var output: File = null
executable = config("exe", default = "bowtie", freeVar = false)
override val versionRegex = """.*[Vv]ersion:? (.*)""".r
......@@ -67,8 +67,13 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
optional("--maxbts", maxbts) +
optional("--maqerr", maqerr) +
required(reference) +
required(R1) +
optional(R2) +
(R2 match {
case Some(r2) => {
required("-1", R1) +
optional("-2", r2)
}
case _ => required(R1)
}) +
" > " + required(output)
}
}
\ No newline at end of file
......@@ -368,7 +368,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
def addBowtie(R1: File, R2: File, output: File, deps: List[File]): File = {
val bowtie = new Bowtie(this)
bowtie.R1 = R1
if (paired) bowtie.R2 = R2
if (paired) bowtie.R2 = Some(R2)
bowtie.deps = deps
bowtie.output = this.swapExt(output.getParent, output, ".bam", ".sam")
bowtie.isIntermediate = true
......
......@@ -3,6 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.mapping
import java.io.File
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions._
import org.apache.commons.io.FileUtils
import org.broadinstitute.gatk.queue.QSettings
import org.scalatest.Matchers
......@@ -12,10 +13,7 @@ import org.testng.annotations.{ AfterClass, DataProvider, Test }
import nl.lumc.sasc.biopet.core.config.Config
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaSamse, BwaSampe, BwaAln, BwaMem }
import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, AddOrReplaceReadGroups, MarkDuplicates, SortSam }
import nl.lumc.sasc.biopet.extensions._
import nl.lumc.sasc.biopet.pipelines.flexiprep.Cutadapt
import nl.lumc.sasc.biopet.pipelines.flexiprep.Fastqc
import nl.lumc.sasc.biopet.pipelines.flexiprep._
import nl.lumc.sasc.biopet.pipelines.flexiprep.{ SeqtkSeq, Cutadapt, Fastqc }
import nl.lumc.sasc.biopet.tools.{ Seqstat, FastqSync }
import nl.lumc.sasc.biopet.utils.ConfigUtils
......
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