From a0cf806e232faa293a8842a25293fd15a34a3186 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 21 Oct 2015 09:51:45 +0200
Subject: [PATCH] Fix build issues
---
.../scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index c8b81c0c4..cbe6fd6eb 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -173,19 +173,22 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
def addBedtoolsCounts(bamFile: File, outputPrefix: String, outputDir: File) {
- val bedtoolsSense = BedtoolsCoverage(this, bamFile, squishedCountBed, new File(outputDir, outputPrefix + ".genome.sense.coverage"),
+ val bedtoolsSense = BedtoolsCoverage(this, bamFile, squishedCountBed,
+ output = Some(new File(outputDir, outputPrefix + ".genome.sense.coverage")),
depth = false, sameStrand = true, diffStrand = false)
val countSense = new BedtoolsCoverageToCounts(this)
countSense.input = bedtoolsSense.output
countSense.output = new File(outputDir, outputPrefix + ".genome.sense.counts")
- val bedtoolsAntisense = BedtoolsCoverage(this, bamFile, squishedCountBed, new File(outputDir, outputPrefix + ".genome.antisense.coverage"),
+ val bedtoolsAntisense = BedtoolsCoverage(this, bamFile, squishedCountBed,
+ output = Some(new File(outputDir, outputPrefix + ".genome.antisense.coverage")),
depth = false, sameStrand = false, diffStrand = true)
val countAntisense = new BedtoolsCoverageToCounts(this)
countAntisense.input = bedtoolsAntisense.output
countAntisense.output = new File(outputDir, outputPrefix + ".genome.antisense.counts")
- val bedtools = BedtoolsCoverage(this, bamFile, squishedCountBed, new File(outputDir, outputPrefix + ".genome.coverage"),
+ val bedtools = BedtoolsCoverage(this, bamFile, squishedCountBed,
+ output = Some(new File(outputDir, outputPrefix + ".genome.coverage")),
depth = false, sameStrand = false, diffStrand = false)
val count = new BedtoolsCoverageToCounts(this)
count.input = bedtools.output
--
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