Commit 29f9b30f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Name change

parent 5f8a8375
......@@ -56,7 +56,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
gatkPipeline.biopetScript
addAll(gatkPipeline.functions)
addPerSampleJobs()
addSamplesJobs()
}
def addMultiSampleJobs(): Unit = {
......
......@@ -151,7 +151,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
def biopetScript(): Unit = {
addPerSampleJobs
addSamplesJobs()
}
def addMultiSampleJobs(): Unit = {
......
......@@ -128,7 +128,7 @@ trait MultiSampleQScript extends BiopetQScript {
protected def sampleIds: Set[String] = ConfigUtils.any2map(Config.global.map("samples")).keySet
/** Runs addAndTrackJobs method for each sample */
final def addPerSampleJobs() {
final def addSamplesJobs() {
if (onlySamples.isEmpty) {
samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
addMultiSampleJobs()
......
......@@ -102,7 +102,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript {
// Third step is calling peaks on the bam files produced with the mapping pipeline, this will be done with MACS2
logger.info("Starting CArP pipeline")
addPerSampleJobs
addSamplesJobs()
}
def addMultiSampleJobs(): Unit = {
......
......@@ -30,7 +30,7 @@ class Kopisu(val root: Configurable) extends QScript with MultiSampleQScript {
}
def biopetScript() {
this.addPerSampleJobs()
addSamplesJobs()
}
def makeSample(id: String) = new Sample(id)
......
......@@ -151,7 +151,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
tagsLibrary = cdl.output
}
addPerSampleJobs
addSamplesJobs()
}
def addMultiSampleJobs(): Unit = {
......
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