From cb72d450e5f05da613d2904ea88194fbb564063b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 26 Jun 2014 08:53:27 +0200
Subject: [PATCH] Added Intermediate files
---
.../lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 12 +++++++-----
1 file changed, 7 insertions(+), 5 deletions(-)
diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 1ec7d12ad..aaf4fe352 100644
--- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -121,14 +121,14 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
if (paired) bwaCommand.R2 = fastq_R2
bwaCommand.RG = getReadGroup
bwaCommand.output = new File(outputDir + outputName + ".sam")
- add(bwaCommand)
+ add(bwaCommand, isIntermediate = true)
bamFile = addSortSam(List(bwaCommand.output), swapExt(outputDir,bwaCommand.output,".sam",".bam"), outputDir)
} else if (aligner == "star") {
- val starCommand = Star(this, fastq_R1, if (paired) fastq_R2 else null, outputDir)
+ val starCommand = Star(this, fastq_R1, if (paired) fastq_R2 else null, outputDir, isIntermediate = true)
add(starCommand)
bamFile = addAddOrReplaceReadGroups(List(starCommand.outputSam), new File(outputDir + outputName + ".bam"), outputDir)
} else if (aligner == "star-2pass") {
- val star2pass = Star._2pass(this, fastq_R1, if (paired) fastq_R2 else null, outputDir)
+ val star2pass = Star._2pass(this, fastq_R1, if (paired) fastq_R2 else null, outputDir, isIntermediate = true)
addAll(star2pass._2)
bamFile = addAddOrReplaceReadGroups(List(star2pass._1), new File(outputDir + outputName + ".bam"), outputDir)
} else throw new IllegalStateException("Option Alginer: '" + aligner + "' is not valid")
@@ -145,6 +145,7 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
sortSam.memoryLimit = 2
sortSam.nCoresRequest = 2
sortSam.jobResourceRequests :+= "h_vmem=4G"
+ if (!skipMarkduplicates) sortSam.isIntermediate = true
add(sortSam)
return sortSam.output
@@ -166,6 +167,7 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
addOrReplaceReadGroups.RGSM = RGSM
if (RGCN != null) addOrReplaceReadGroups.RGCN = RGCN
if (RGDS != null) addOrReplaceReadGroups.RGDS = RGDS
+ if (!skipMarkduplicates) addOrReplaceReadGroups.isIntermediate = true
add(addOrReplaceReadGroups)
return addOrReplaceReadGroups.output
@@ -200,13 +202,13 @@ class Mapping(val root:Configurable) extends QScript with BiopetQScript {
}
def loadRunConfig(runConfig:Map[String,Any], sampleConfig:Map[String,Any], runDir: String) {
- //config = Config.mergeConfigs(globalConfig.getAsConfig("mapping"), globalConfig)
+ logger.debug("Mapping runconfig: " + runConfig)
var inputType = ""
if (runConfig.contains("inputtype")) inputType = runConfig("inputtype").toString
else inputType = config("inputtype", "dna")
if (inputType == "rna") aligner = config("rna_aligner", "star-2pass")
if (runConfig.contains("R1")) input_R1 = runConfig("R1").toString
- if (runConfig.contains("R2")) input_R1 = runConfig("R2").toString
+ if (runConfig.contains("R2")) input_R2 = runConfig("R2").toString
paired = (input_R2 != null)
RGLB = runConfig("ID").toString
RGSM = sampleConfig("ID").toString
--
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