From ef811002ef70f894c468a11840cb5b9a0d3625ca Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Tue, 10 May 2016 16:01:53 +0200
Subject: [PATCH] fix typo
---
.../shiva/svcallers/Breakdancer.scala | 10 ++---
.../pipelines/shiva/svcallers/Clever.scala | 10 ++---
.../pipelines/shiva/svcallers/Delly.scala | 40 +++++++++----------
.../pipelines/shiva/svcallers/Pindel.scala | 10 ++---
4 files changed, 35 insertions(+), 35 deletions(-)
diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
index 8a14292a1..f44ec38c9 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
@@ -35,13 +35,13 @@ class Breakdancer(val root: Configurable) extends SvCaller {
val bdvcf = BreakdancerVCF(this, breakdancer.output, new File(breakdancerSampleDir, sample + ".breakdancer.vcf"),
sample = sample + "_bd")
- val compresssedVCF = new SortVcf(this)
- compresssedVCF.input = bdvcf.output
- compresssedVCF.output = new File(breakdancerSampleDir, s"${sample}.breakdancer.vcf.gz")
+ val compressedVCF = new SortVcf(this)
+ compressedVCF.input = bdvcf.output
+ compressedVCF.output = new File(breakdancerSampleDir, s"${sample}.breakdancer.vcf.gz")
- add(bdcfg, breakdancer, bdvcf, compresssedVCF)
+ add(bdcfg, breakdancer, bdvcf, compressedVCF)
- addVCF(sample, compresssedVCF.output)
+ addVCF(sample, compressedVCF.output)
}
}
}
diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
index 606287478..3c5dc47bc 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
@@ -37,12 +37,12 @@ class Clever(val root: Configurable) extends SvCaller {
cleverVCF.isIntermediate = true
add(cleverVCF)
- val sortvcf = new SortVcf(this)
- sortvcf.input = cleverVCF.output
- sortvcf.output = new File(cleverDir, s"${sample}.clever.vcf.gz")
- add(sortvcf)
+ val compressedVCF = new SortVcf(this)
+ compressedVCF.input = cleverVCF.output
+ compressedVCF.output = new File(cleverDir, s"${sample}.clever.vcf.gz")
+ add(compressedVCF)
- addVCF(sample, sortvcf.output)
+ addVCF(sample, compressedVCF.output)
}
}
}
diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
index 7589d9f86..221b062b3 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
@@ -43,12 +43,12 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.del.vcf")
add(delly)
- val compresssedVCF = new SortVcf(this)
- compresssedVCF.input = delly.outputvcf
- compresssedVCF.output = new File(dellyDir, s"${sample}.delly.del.vcf.gz")
- add(compresssedVCF)
+ val compressedVCF = new SortVcf(this)
+ compressedVCF.input = delly.outputvcf
+ compressedVCF.output = new File(dellyDir, s"${sample}.delly.del.vcf.gz")
+ add(compressedVCF)
- catVariants.variant :+= compresssedVCF.output
+ catVariants.variant :+= compressedVCF.output
}
if (dup) {
val delly = new DellyCaller(this)
@@ -57,12 +57,12 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.dup.vcf")
add(delly)
- val compresssedVCF = new SortVcf(this)
- compresssedVCF.input = delly.outputvcf
- compresssedVCF.output = new File(dellyDir, s"${sample}.delly.dup.vcf.gz")
- add(compresssedVCF)
+ val compressedVCF = new SortVcf(this)
+ compressedVCF.input = delly.outputvcf
+ compressedVCF.output = new File(dellyDir, s"${sample}.delly.dup.vcf.gz")
+ add(compressedVCF)
- catVariants.variant :+= compresssedVCF.output
+ catVariants.variant :+= compressedVCF.output
}
if (inv) {
val delly = new DellyCaller(this)
@@ -71,12 +71,12 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.inv.vcf")
add(delly)
- val compresssedVCF = new SortVcf(this)
- compresssedVCF.input = delly.outputvcf
- compresssedVCF.output = new File(dellyDir, s"${sample}.delly.inv.vcf.gz")
- add(compresssedVCF)
+ val compressedVCF = new SortVcf(this)
+ compressedVCF.input = delly.outputvcf
+ compressedVCF.output = new File(dellyDir, s"${sample}.delly.inv.vcf.gz")
+ add(compressedVCF)
- catVariants.variant :+= compresssedVCF.output
+ catVariants.variant :+= compressedVCF.output
}
if (tra) {
val delly = new DellyCaller(this)
@@ -85,12 +85,12 @@ class Delly(val root: Configurable) extends SvCaller {
delly.outputvcf = new File(dellyDir, sample + ".delly.tra.vcf")
add(delly)
- val compresssedVCF = new SortVcf(this)
- compresssedVCF.input = delly.outputvcf
- compresssedVCF.output = new File(dellyDir, s"${sample}.delly.tra.vcf.gz")
- add(compresssedVCF)
+ val compressedVCF = new SortVcf(this)
+ compressedVCF.input = delly.outputvcf
+ compressedVCF.output = new File(dellyDir, s"${sample}.delly.tra.vcf.gz")
+ add(compressedVCF)
- catVariants.variant :+= compresssedVCF.output
+ catVariants.variant :+= compressedVCF.output
}
require(catVariants.variant.nonEmpty, "At least 1 SV-type should be selected for Delly")
diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
index ff6fb17d0..c83ee46b7 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala
@@ -59,12 +59,12 @@ class Pindel(val root: Configurable) extends SvCaller {
pindelVcf.outputVCF = new File(pindelDir, s"${sample}.pindel.vcf")
add(pindelVcf)
- val compresssedVCF = new SortVcf(this)
- compresssedVCF.input = pindelVcf.outputVCF
- compresssedVCF.output = new File(pindelDir, s"${sample}.pindel.vcf.gz")
- add(compresssedVCF)
+ val compressedVCF = new SortVcf(this)
+ compressedVCF.input = pindelVcf.outputVCF
+ compressedVCF.output = new File(pindelDir, s"${sample}.pindel.vcf.gz")
+ add(compressedVCF)
- addVCF(sample, compresssedVCF.output)
+ addVCF(sample, compressedVCF.output)
}
}
--
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