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Passing the ADPR R script to FCPTest. 

Changed the FCP.q to use an InProcessFunction work around the -runDir issue GSA-420.
Tested the FCPTest using the following dotkits and "ant clean pipelinetest -Dpipeline.run=run":
  - R-2.11
  - Oracle-full-client
  - .cx-oracle-5.0.2-python-2.6.5-oracle-full-client-11.1


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5029 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-01-20 06:08:45 +00:00
parent 7087c2f422
commit 4d611e53e7
2 changed files with 28 additions and 13 deletions
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37
scala/qscript/playground/fullCallingPipeline.q
View File

@ -48,7 +48,7 @@ class fullCallingPipeline extends QScript {
var skip_cleaning = false
@Input(doc="ADPR script", shortName ="tearScript", required=true)
var adprthing: File = _
var tearScript: File = _
//@Input(doc="Sequencing maching name (for use by adpr)")
//var machine: String = _
@ -200,18 +200,10 @@ class fullCallingPipeline extends QScript {
}
}
//def endToEnd(base: String, bamType: String, adprthing: File, seqinfo: String, exptype: String) = {
def endToEnd(base: String, bamType: String) = {
val samples = qscript.pipeline.getSamples.filter(_.getBamFiles.contains(bamType)).toList
val bamFiles = samples.map(_.getBamFiles.get(bamType))
val listOfBams = new File(base +".BamFiles.list")
val writer = new PrintWriter(listOfBams)
for (bamFile <- bamFiles){
writer.println(bamFile.toString)
}
writer.close()
// step through the un-indel-cleaned graph:
// 1a. call snps and indels
@ -385,7 +377,28 @@ class fullCallingPipeline extends QScript {
}
add(snps)
// 5. Run the ADPR and make pretty stuff
// 5. Make the bam list
val listOfBams = new File(base +".BamFiles.list")
class BamListWriter extends InProcessFunction {
@Input(doc="bamFiles") var bamFiles: List[File] = Nil
@Output(doc="bamList") var bamList: File = _
def run {
val writer = new PrintWriter(bamList)
for (bamFile <- bamFiles)
writer.println(bamFile.toString)
writer.close()
}
}
val writeBamList = new BamListWriter
writeBamList.bamFiles = bamFiles
writeBamList.bamList = listOfBams
writeBamList.analysisName = base + "_BamList"
writeBamList.jobOutputFile = new File(".queue/logs/SNPCalling/bamlist.out")
// 6. Run the ADPR and make pretty stuff
class rCommand extends CommandLineFunction{
@Argument(doc="R script")
@ -404,7 +417,7 @@ class fullCallingPipeline extends QScript {
val adpr = new rCommand
adpr.bamlist = listOfBams
adpr.script = adprthing
adpr.script = tearScript
adpr.evalroot = eval.reportLocation
adpr.jobOutputFile = new File(".queue/logs/SNPCalling/adpr.out")
adpr.tearsheet = new File("SnpCalls", base + ".tearsheet.pdf")
@ -416,6 +429,6 @@ class fullCallingPipeline extends QScript {
add(igv2)
}
add(mergeIndels,annotated,masker,handFilter,eval,adpr)
add(mergeIndels,annotated,masker,handFilter,eval,writeBamList,adpr)
}
}

4
scala/test/org/broadinstitute/sting/queue/pipeline/FullCallingPipelineTest.scala
View File

@ -90,10 +90,12 @@ class FullCallingPipelineTest extends BaseTest {
var cleanType = "cleaned"
// Run the pipeline with the expected inputs.
val currentDir = new File(".").getAbsolutePath
var pipelineCommand = ("-retry 1 -S scala/qscript/playground/fullCallingPipeline.q" +
" -jobProject %s -Y %s -refseqTable %s" +
" -tearScript %s/R/DataProcessingReport/GetTearsheetStats.R" +
" --gatkjar %s/dist/GenomeAnalysisTK.jar")
.format(projectName, yamlFile, dataset.refseq, new File(".").getAbsolutePath)
.format(projectName, yamlFile, dataset.refseq, currentDir, currentDir)
if (!dataset.runIndelRealigner) {
pipelineCommand += " -skipCleaning"