Commit c18e88d9 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adds finalBamFile function

parent 89b2c3cd
......@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import java.io.File
import java.util.Date
import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
import nl.lumc.sasc.biopet.extensions.{ Star, Stampy, Bowtie }
import nl.lumc.sasc.biopet.extensions.{ Ln, Star, Stampy, Bowtie }
import nl.lumc.sasc.biopet.extensions.bwa.{ BwaSamse, BwaSampe, BwaAln, BwaMem }
import nl.lumc.sasc.biopet.tools.FastqSplitter
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, SortSam, MergeSamFiles, AddOrReplaceReadGroups }
......@@ -92,6 +92,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
protected var paired: Boolean = false
val flexiprep = new Flexiprep(this)
def finalBamFile: File = outputDir + outputName + ".final.bam"
def init() {
if (outputDir == null) throw new IllegalStateException("Missing Output directory on mapping module")
......@@ -209,6 +210,8 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
if (!skipMetrics) addAll(BamMetrics(this, bamFile, outputDir + "metrics/").functions)
add(Ln(this, swapExt(outputDir, bamFile, ".bam", ".bai"), swapExt(outputDir, finalBamFile, ".bam", ".bai")))
add(Ln(this, bamFile, finalBamFile))
outputFiles += ("finalBamFile" -> bamFile)
}
......
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