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Commit ccf09c1a authored by Wai Yi Leung's avatar Wai Yi Leung
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Fixes in summary, newline and introduce RPKMonly option to generate rpkm files..

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public/kopisu/Kopisu.iml deleted 100644 → 0
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\ No newline at end of file
public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
+ 36
− 29
View file @ ccf09c1a
......@@ -26,7 +26,9 @@ import org.broadinstitute.gatk.queue.QScript
import scala.io.Source
class ConiferPipeline(val root: Configurable) extends QScript with BiopetQScript {
//*
// Kopisu - Coniferpipeline is a pipeline that can run standalone
// */
def this() = this(null)
/** Input bamfile */
......@@ -39,11 +41,14 @@ class ConiferPipeline(val root: Configurable) extends QScript with BiopetQScript
var sampleLabel: String = _
/** Exon definitions in bed format */
@Input(doc = "Exon definition file in bed format", fullName = "exon_bed", shortName = "bed", required = true)
var probeFile: File = _
@Input(doc = "Exon definition file in bed format", fullName = "exon_bed", shortName = "bed", required = false)
var probeFile: File = config("probeFile")
@Input(doc = "Previous RPKM files (controls)", fullName = "rpkm_controls", shortName = "rc", required = false)
var controlsDir: File = config("controlsDir")
@Input(doc = "Previous RPKM files (controls)", fullName = "rpkm_controls", shortName = "rc", required = true)
var rpkmControls: File = _
@Argument(doc = "Enable RPKM only mode, generate files for reference db", shortName = "rpkmonly", required = false)
var RPKMonly: Boolean = false
val summary = new ConiferSummary(this)
......@@ -78,35 +83,37 @@ class ConiferPipeline(val root: Configurable) extends QScript with BiopetQScript
coniferRPKM.output = new File(RPKMdir + File.separator + input2RPKM(inputBam))
add(coniferRPKM)
/** Collect the rpkm_output to a temp directory, where we merge with the control files */
var refRPKMlist: List[File] = Nil
for (f <- rpkmControls.listFiles()) {
var target = new File(RPKMdir + File.separator + f.getName)
if (!target.exists()) {
logger.info("Creating " + target.getAbsolutePath)
add(Ln(this, f, target, true))
refRPKMlist :+= target
if (!RPKMonly) {
/** Collect the rpkm_output to a temp directory, where we merge with the control files */
var refRPKMlist: List[File] = Nil
for (f <- controlsDir.listFiles()) {
var target = new File(RPKMdir + File.separator + f.getName)
if (!target.exists()) {
logger.info("Creating " + target.getAbsolutePath)
add(Ln(this, f, target, true))
refRPKMlist :+= target
}
}
}
val coniferAnalyze = new ConiferAnalyze(this)
coniferAnalyze.deps = List(coniferRPKM.output) ++ refRPKMlist
coniferAnalyze.probes = this.probeFile
coniferAnalyze.rpkmDir = RPKMdir
coniferAnalyze.output = new File(sampleDir + File.separator + input2HDF5(inputBam))
add(coniferAnalyze)
val coniferAnalyze = new ConiferAnalyze(this)
coniferAnalyze.deps = List(coniferRPKM.output) ++ refRPKMlist
coniferAnalyze.probes = this.probeFile
coniferAnalyze.rpkmDir = RPKMdir
coniferAnalyze.output = new File(sampleDir + File.separator + input2HDF5(inputBam))
add(coniferAnalyze)
val coniferCall = new ConiferCall(this)
coniferCall.input = coniferAnalyze.output
coniferCall.output = new File(sampleDir + File.separator + "calls.txt")
add(coniferCall)
val coniferCall = new ConiferCall(this)
coniferCall.input = coniferAnalyze.output
coniferCall.output = new File(sampleDir + File.separator + "calls.txt")
add(coniferCall)
summary.deps = List(coniferCall.output)
summary.label = sampleLabel
summary.calls = coniferCall.output
summary.out = new File(sampleDir + File.separator + input2Calls(inputBam))
summary.deps = List(coniferCall.output)
summary.label = sampleLabel
summary.calls = coniferCall.output
summary.out = new File(sampleDir + File.separator + input2Calls(inputBam))
add(summary)
add(summary)
}
}
}
......
public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
+ 2
− 1
View file @ ccf09c1a
......@@ -31,10 +31,11 @@ class ConiferSummary(val root: Configurable) extends InProcessFunction with Conf
for (line <- Source.fromFile(callFile).getLines()) {
line.startsWith(sampleName) || line.startsWith("sampleID") match {
case true => writer.write(line)
case true => writer.write(line + "\n");
case _ =>
}
}
writer.close()
}
this.analysisName = getClass.getSimpleName
......
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