From 4785e578d4a2613199cd142aa03d3f740fd37f9b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 20 May 2014 13:07:03 +0200
Subject: [PATCH] - Fixed input field on markduplicates in mapping module
---
.../biopet/pipelines/mapping/Mapping.scala | 32 +++++++++----------
1 file changed, 16 insertions(+), 16 deletions(-)
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 7f680b3a6..915c7360f 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/java/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -84,11 +84,11 @@ class Mapping(private var globalConfig: Config) extends QScript {
val bwaCommand = new Bwa(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2;
RG = getReadGroup; output = new File(outputDir + outputName + ".sam") }
add(bwaCommand)
- bamFile = addAddOrReplaceReadGroups(List(bwaCommand.output), swapExt(outputDir,bwaCommand.output,".sam",".bam"), outputDir)
+ bamFile = addSortSam(List(bwaCommand.output), swapExt(outputDir,bwaCommand.output,".sam",".bam"), outputDir)
} else if (aligner == "star") {
val starCommand = new Star(config) { R1 = fastq_R1; if (paired) R2 = fastq_R2; this.outputDir = outputDir }
add(starCommand)
- bamFile = addSortSam(List(starCommand.outputSam), swapExt(outputDir,starCommand.outputSam,".sam",".bam"), outputDir)
+ bamFile = addAddOrReplaceReadGroups(List(starCommand.outputSam), swapExt(outputDir,starCommand.outputSam,".sam",".bam"), outputDir)
}
if (!skipMarkduplicates) bamFile = addMarkDuplicates(List(bamFile), swapExt(outputDir,bamFile,".bam",".dedup.bam"), outputDir)
@@ -110,12 +110,12 @@ class Mapping(private var globalConfig: Config) extends QScript {
def addAddOrReplaceReadGroups(inputSam:List[File], outputFile:File, dir:String) : File = {
val addOrReplaceReadGroups = new AddOrReplaceReadGroups {
- input = inputSam
- output = outputFile
- createIndex = true
- memoryLimit = 2
- nCoresRequest = 2
- jobResourceRequests :+= "h_vmem=4G"
+ this.input = inputSam
+ this.output = outputFile
+ this.createIndex = true
+ this.memoryLimit = 2
+ this.nCoresRequest = 2
+ this.jobResourceRequests :+= "h_vmem=4G"
this.RGLB = RGLB
this.RGPL = RGPL
@@ -127,15 +127,15 @@ class Mapping(private var globalConfig: Config) extends QScript {
return addOrReplaceReadGroups.output
}
- def addMarkDuplicates(inputBams:List[File], outputFile:File, dir:String) : File = {
+ def addMarkDuplicates(input_Bams:List[File], outputFile:File, dir:String) : File = {
val markDuplicates = new MarkDuplicates {
- input = inputBams
- output = outputFile
- REMOVE_DUPLICATES = false
- metrics = swapExt(dir,outputFile,".bam",".metrics")
- outputIndex = swapExt(dir,this.output,".bam",".bai")
- memoryLimit = 2
- jobResourceRequests :+= "h_vmem=4G"
+ this.input = input_Bams
+ this.output = outputFile
+ this.REMOVE_DUPLICATES = false
+ this.metrics = swapExt(dir,outputFile,".bam",".metrics")
+ this.outputIndex = swapExt(dir,this.output,".bam",".bai")
+ this.memoryLimit = 2
+ this.jobResourceRequests :+= "h_vmem=4G"
}
add(markDuplicates)
--
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