From 64d1f13ac4ef6b80cf68d3537ff9e7c0d4689b75 Mon Sep 17 00:00:00 2001
From: wyleung <w.y.leung@e-sensei.nl>
Date: Fri, 24 Oct 2014 15:07:48 +0200
Subject: [PATCH] Renames
---
.../lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala | 6 +++---
.../scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
index a6233d71f..631e9d33b 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/svcallers/Breakdancer.scala
@@ -194,17 +194,17 @@ class Breakdancer(val root: Configurable) extends QScript with BiopetQScript {
val bdcfg = BreakdancerConfig(this, input, this.configfile)
bdcfg.deps = this.deps
- outputFiles += ("breakdancer_cfg" -> bdcfg.output )
+ outputFiles += ("cfg" -> bdcfg.output )
add( bdcfg )
val output_tsv: File = this.outputraw
val breakdancer = BreakdancerCaller( this, bdcfg.output, output_tsv )
add( breakdancer )
- outputFiles += ("breakdancer_tsv" -> breakdancer.output )
+ outputFiles += ("tsv" -> breakdancer.output )
val bdvcf = BreakdancerVCF( this, breakdancer.output, this.outputvcf )
add( bdvcf )
- outputFiles += ("breakdancer_vcf" -> bdvcf.output )
+ outputFiles += ("vcf" -> bdvcf.output )
}
}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index 3c00eb3cc..b647ab4ed 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -101,7 +101,7 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
val breakdancerDir = svcallingDir + sampleID + ".breakdancer/"
val breakdancer = Breakdancer(this, bamFile, this.reference, breakdancerDir)
- sampleOutput.vcf += ("breakdancer" -> List(breakdancer.outputraw))
+ sampleOutput.vcf += ("breakdancer" -> List(breakdancer.outputvcf))
addAll(breakdancer.functions)
// for pindel we should use per library config collected into one config file
--
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