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Added test mode to DPP 

* in test mode, no @PG tags are output to the final bam file
* updated pipeline test to use -test mode.
* MD5s are now dependent on BWA version
This commit is contained in:
Mauricio Carneiro 2011-12-12 12:35:36 -05:00
parent a70a0f25fb
commit a3c3d72313
2 changed files with 10 additions and 2 deletions
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6
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
View File

@ -83,6 +83,10 @@ class DataProcessingPipeline extends QScript {
@Input(doc="Define the default platform for Count Covariates -- useful for techdev purposes only.", fullName="default_platform", shortName="dp", required=false) @Input(doc="Define the default platform for Count Covariates -- useful for techdev purposes only.", fullName="default_platform", shortName="dp", required=false)
var defaultPlatform: String = "" var defaultPlatform: String = ""
@Hidden
@Input(doc="Run the pipeline in test mode only", fullName = "test_mode", shortName = "test", required=false)
var testMode: Boolean = false
/**************************************************************************** /****************************************************************************
* Global Variables * Global Variables
@ -335,6 +339,7 @@ class DataProcessingPipeline extends QScript {
this.known ++= qscript.indels this.known ++= qscript.indels
this.consensusDeterminationModel = cleanModelEnum this.consensusDeterminationModel = cleanModelEnum
this.compress = 0 this.compress = 0
this.noPGTag = qscript.testMode;
this.scatterCount = nContigs this.scatterCount = nContigs
this.analysisName = queueLogDir + outBam + ".clean" this.analysisName = queueLogDir + outBam + ".clean"
this.jobName = queueLogDir + outBam + ".clean" this.jobName = queueLogDir + outBam + ".clean"
@ -360,6 +365,7 @@ class DataProcessingPipeline extends QScript {
this.out = outBam this.out = outBam
if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString) if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
else if (qscript.intervals != null) this.intervals :+= qscript.intervals else if (qscript.intervals != null) this.intervals :+= qscript.intervals
this.no_pg_tag = qscript.testMode
this.scatterCount = nContigs this.scatterCount = nContigs
this.isIntermediate = false this.isIntermediate = false
this.analysisName = queueLogDir + outBam + ".recalibration" this.analysisName = queueLogDir + outBam + ".recalibration"

6
public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
View File

@ -40,8 +40,9 @@ class DataProcessingPipelineTest {
" -i " + BaseTest.testDir + "exampleBAM.bam", " -i " + BaseTest.testDir + "exampleBAM.bam",
" -D " + BaseTest.testDir + "exampleDBSNP.vcf", " -D " + BaseTest.testDir + "exampleDBSNP.vcf",
" -nv ", " -nv ",
" -test ",
" -p " + projectName).mkString " -p " + projectName).mkString
spec.fileMD5s += testOut -> "a9769a85f15e77505835068353ce4788" spec.fileMD5s += testOut -> "1f85e76de760167a77ed1d9ab4da2936"
PipelineTest.executeTest(spec) PipelineTest.executeTest(spec)
} }
@ -57,10 +58,11 @@ class DataProcessingPipelineTest {
" -i " + BaseTest.testDir + "exampleBAM.bam", " -i " + BaseTest.testDir + "exampleBAM.bam",
" -D " + BaseTest.testDir + "exampleDBSNP.vcf", " -D " + BaseTest.testDir + "exampleDBSNP.vcf",
" -nv ", " -nv ",
" -test ",
" -bwa /home/unix/carneiro/bin/bwa", " -bwa /home/unix/carneiro/bin/bwa",
" -bwape ", " -bwape ",
" -p " + projectName).mkString " -p " + projectName).mkString
spec.fileMD5s += testOut -> "fad1fd2e69287c1beb423ce17fa464d6" spec.fileMD5s += testOut -> "57416a0abdf9524bc92834d466529708"
PipelineTest.executeTest(spec) PipelineTest.executeTest(spec)
} }