From fa32164fcea2bff675361820b68540ee5084f48a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 4 Feb 2015 11:51:10 +0100
Subject: [PATCH] Change some options
---
.../sasc/biopet/pipelines/sage/Sage.scala | 23 ++++++++-----------
1 file changed, 9 insertions(+), 14 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 a614d61d4..e51be1d71 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
@@ -36,11 +36,8 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
def this() = this(null)
var countBed: Option[File] = config("count_bed")
-
- var squishedCountBed: Option[File] = config("squished_count_bed")
-
+ var squishedCountBed: File = _
var transcriptome: Option[File] = config("transcriptome")
-
var tagsLibrary: Option[File] = config("tags_library")
override def defaults = ConfigUtils.mergeMaps(Map("bowtie" -> Map(
@@ -129,16 +126,14 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
if (!outputDir.endsWith("/")) outputDir += "/"
if (transcriptome.isEmpty && tagsLibrary.isEmpty)
throw new IllegalStateException("No transcriptome or taglib found")
- if (countBed.isEmpty && squishedCountBed.isEmpty)
- throw new IllegalStateException("No bedfile supplied, please add a countBed or squishedCountBed")
+ if (countBed.isEmpty)
+ throw new IllegalStateException("No bedfile supplied, please add a countBed")
}
def biopetScript() {
- if (squishedCountBed.isEmpty) {
- val squishBed = SquishBed(this, countBed.get, outputDir)
- add(squishBed)
- squishedCountBed = Some(squishBed.output)
- }
+ val squishBed = SquishBed(this, countBed.get, outputDir)
+ add(squishBed)
+ squishedCountBed = squishBed.output
if (tagsLibrary.isEmpty) {
val cdl = new SageCreateLibrary(this)
@@ -158,19 +153,19 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
}
def addBedtoolsCounts(bamFile: File, outputPrefix: String, outputDir: String) {
- val bedtoolsSense = BedtoolsCoverage(this, bamFile, squishedCountBed.get, outputDir + outputPrefix + ".genome.sense.coverage",
+ val bedtoolsSense = BedtoolsCoverage(this, bamFile, squishedCountBed, outputDir + outputPrefix + ".genome.sense.coverage",
depth = false, sameStrand = true, diffStrand = false)
val countSense = new BedtoolsCoverageToCounts(this)
countSense.input = bedtoolsSense.output
countSense.output = outputDir + outputPrefix + ".genome.sense.counts"
- val bedtoolsAntisense = BedtoolsCoverage(this, bamFile, squishedCountBed.get, outputDir + outputPrefix + ".genome.antisense.coverage",
+ val bedtoolsAntisense = BedtoolsCoverage(this, bamFile, squishedCountBed, outputDir + outputPrefix + ".genome.antisense.coverage",
depth = false, sameStrand = false, diffStrand = true)
val countAntisense = new BedtoolsCoverageToCounts(this)
countAntisense.input = bedtoolsAntisense.output
countAntisense.output = outputDir + outputPrefix + ".genome.antisense.counts"
- val bedtools = BedtoolsCoverage(this, bamFile, squishedCountBed.get, outputDir + outputPrefix + ".genome.coverage",
+ val bedtools = BedtoolsCoverage(this, bamFile, squishedCountBed, outputDir + outputPrefix + ".genome.coverage",
depth = false, sameStrand = false, diffStrand = false)
val count = new BedtoolsCoverageToCounts(this)
count.input = bedtools.output
--
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