Commit 7f1ff523 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix outputDirs

parent 28b42baf
......@@ -50,8 +50,8 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
}
def biopetScript() {
add(SamtoolsFlagstat(this, inputBam, outputDir))
add(BiopetFlagstat(this, inputBam, outputDir))
add(SamtoolsFlagstat(this, inputBam, swapExt(outputDir, inputBam, ".bam", ".flagstat")))
add(BiopetFlagstat(this, inputBam, swapExt(outputDir, inputBam, ".bam", ".biopetflagstat")))
add(CollectGcBiasMetrics(this, inputBam, outputDir))
add(CollectInsertSizeMetrics(this, inputBam, outputDir))
add(CollectAlignmentSummaryMetrics(this, inputBam, outputDir))
......@@ -69,13 +69,13 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
val strictOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.strict.bam")
add(BedtoolsIntersect(this, inputBam, bedFile, strictOutputBam, minOverlap = config("strictintersectoverlap", default = 1.0)), true)
add(SamtoolsFlagstat(this, strictOutputBam))
add(BiopetFlagstat(this, strictOutputBam, targetDir))
add(SamtoolsFlagstat(this, strictOutputBam, swapExt(targetDir, strictOutputBam, ".bam", ".flagstat")))
add(BiopetFlagstat(this, strictOutputBam, swapExt(targetDir, strictOutputBam, ".bam", ".biopetflagstat")))
val looseOutputBam = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".overlap.loose.bam")
add(BedtoolsIntersect(this, inputBam, bedFile, looseOutputBam, minOverlap = config("looseintersectoverlap", default = 0.01)), true)
add(SamtoolsFlagstat(this, looseOutputBam))
add(BiopetFlagstat(this, looseOutputBam, targetDir))
add(SamtoolsFlagstat(this, looseOutputBam, swapExt(targetDir, looseOutputBam, ".bam", ".biopet")))
add(BiopetFlagstat(this, looseOutputBam, swapExt(targetDir, looseOutputBam, ".bam", ".biopetflagstat")))
val coverageFile = new File(targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
add(BedtoolsCoverage(this, inputBam, bedFile, coverageFile, true), true)
......
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