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Added test mode to PPP 

* in test mode, no @PG tags are output to the final bam file
* updated pipeline test to use -test mode.
* MD5s updated accordingly
This commit is contained in:
Mauricio Carneiro 2011-12-12 18:08:29 -05:00
parent a3c3d72313
commit 663184ee9d
2 changed files with 7 additions and 1 deletions
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5
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
View File

@ -47,6 +47,10 @@ class PacbioProcessingPipeline extends QScript {
@Input(shortName="bwastring", required=false) @Input(shortName="bwastring", required=false)
var bwastring: String = "" var bwastring: String = ""
@Hidden
@Input(shortName = "test", fullName = "test_mode", required = false)
var testMode: Boolean = false
val queueLogDir: String = ".qlog/" val queueLogDir: String = ".qlog/"
def script = { def script = {
@ -170,6 +174,7 @@ class PacbioProcessingPipeline extends QScript {
this.input_file :+= inBam this.input_file :+= inBam
this.recal_file = inRecalFile this.recal_file = inRecalFile
this.out = outBam this.out = outBam
this.no_pg_tag = testMode
this.isIntermediate = false this.isIntermediate = false
this.analysisName = queueLogDir + outBam + ".recalibration" this.analysisName = queueLogDir + outBam + ".recalibration"
this.jobName = queueLogDir + outBam + ".recalibration" this.jobName = queueLogDir + outBam + ".recalibration"

3
public/scala/test/org/broadinstitute/sting/queue/pipeline/PacbioProcessingPipelineTest.scala
View File

@ -38,8 +38,9 @@ class PacbioProcessingPipelineTest {
" -R " + BaseTest.testDir + "exampleFASTA.fasta", " -R " + BaseTest.testDir + "exampleFASTA.fasta",
" -i " + BaseTest.testDir + "exampleBAM.bam", " -i " + BaseTest.testDir + "exampleBAM.bam",
" -blasr ", " -blasr ",
" -test ",
" -D " + BaseTest.testDir + "exampleDBSNP.vcf").mkString " -D " + BaseTest.testDir + "exampleDBSNP.vcf").mkString
spec.fileMD5s += testOut -> "3a23c96063743ddbc35897331433e205" spec.fileMD5s += testOut -> "f0adce660b55cb91d5f987f9a145471e"
PipelineTest.executeTest(spec) PipelineTest.executeTest(spec)
} }
} }