Commit a1f5260d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Format change

parent e3b3e129
......@@ -22,9 +22,7 @@ import nl.lumc.sasc.biopet.core.summary.{ SummaryQScript, Summarizable }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.utils.commandline.{ Argument }
/**
* This trait creates a structured way of use multisample pipelines
*/
/** This trait creates a structured way of use multisample pipelines */
trait MultiSampleQScript extends SummaryQScript {
qscript =>
......@@ -41,19 +39,12 @@ trait MultiSampleQScript extends SummaryQScript {
/** Overrules config of qscript with default sample */
val config = new ConfigFunctions(defaultSample = sampleId)
/**
* Library class with basic functions build in
* @param libId
*/
/** Library class with basic functions build in */
abstract class AbstractLibrary(val libId: String) extends Summarizable {
/** Overrules config of qscript with default sample and default library */
val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libId)
/**
* Name overules the one from qscript
* @param summarizable
* @param name
*/
/** Name overules the one from qscript */
def addSummarizable(summarizable: Summarizable, name: String): Unit = {
qscript.addSummarizable(summarizable, name, Some(sampleId), Some(libId))
}
......@@ -162,7 +153,7 @@ trait MultiSampleQScript extends SummaryQScript {
}
/**
* Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given
* Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given.
*/
def addMultiSampleJobs()
......
......@@ -11,16 +11,10 @@ import nl.lumc.sasc.biopet.core.config.Configurable
*/
trait Summarizable {
/**
* Must return files to store into summary
* @return
*/
/** Must return files to store into summary */
def summaryFiles: Map[String, File]
/**
* Must returns stats to store into summary
* @return
*/
/** Must returns stats to store into summary */
def summaryStats: Map[String, Any]
/**
......
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