From 7f1ff5232075e6422f2d6b520b9bfb6eab9aa393 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 16 Feb 2015 19:32:43 +0100
Subject: [PATCH] Fix outputDirs
---
.../biopet/pipelines/bammetrics/BamMetrics.scala | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index f16db9b0e..9dae6e494 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -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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