Commit 4db37226 authored by Sander Bollen's avatar Sander Bollen

autostyle fixes

parent 7e0576ae
......@@ -115,7 +115,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
if (samples.contains(father)) {
if (samples(father).gender != Gender.Male)
Logging.addError(s"Father of $sampleId is not a male")
} else logger.warn(s"For sample '$sampleId' is father '$father' not found in config")
} else logger.warn(s"For sample '$sampleId' is father '$father' not found in config")
}
g
}
......
package nl.lumc.sasc.biopet.core
import java.io.File
import java.nio.file.Paths
import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
import nl.lumc.sasc.biopet.core.extensions.Md5sum
import nl.lumc.sasc.biopet.utils.config.Config
import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
import org.broadinstitute.gatk.queue.{QScript, QSettings}
import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
import org.broadinstitute.gatk.queue.{ QScript, QSettings }
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
......@@ -18,8 +17,8 @@ import scala.collection.mutable.ListBuffer
import scala.io.Source
/**
* Created by Sander Bollen on 11-4-17.
*/
* Created by Sander Bollen on 11-4-17.
*/
class PedigreeQScriptTest extends TestNGSuite with Matchers {
import PedigreeQScriptTest._
......@@ -145,7 +144,6 @@ object PedigreeQScriptTest {
Paths.get(getClass.getResource(p).toURI).toString
}
val sample1 = Map("samples" ->
Map("sample1" ->
Map("tags" ->
......@@ -180,7 +178,6 @@ object PedigreeQScriptTest {
val trioPed = Map("ped_file" -> resourcePath("/trio.ped"))
def apply(configs: List[Map[String, Any]], only: List[String] = Nil) = {
new QScript with PedigreeQscript { qscript =>
......@@ -215,10 +212,10 @@ object PedigreeQScriptTest {
}
/**
* Factory method for Library class
* @param id SampleId
* @return Sample class
*/
* Factory method for Library class
* @param id SampleId
* @return Sample class
*/
def makeLibrary(id: String): Library = new Library(id)
/** Function to add sample jobs */
......@@ -236,17 +233,17 @@ object PedigreeQScriptTest {
}
/**
* 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(): Unit = {
add(new Md5sum(qscript))
}
/**
* Factory method for Sample class
* @param id SampleId
* @return Sample class
*/
* Factory method for Sample class
* @param id SampleId
* @return Sample class
*/
def makeSample(id: String): Sample = new Sample(id)
/** Must return a map with used settings for this pipeline */
......
......@@ -4,7 +4,7 @@ import java.nio.file.Paths
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.gatk.DepthOfCoverage
import nl.lumc.sasc.biopet.extensions.wisecondor.{WisecondorCount, WisecondorNewRef}
import nl.lumc.sasc.biopet.extensions.wisecondor.{ WisecondorCount, WisecondorNewRef }
import nl.lumc.sasc.biopet.extensions.xhmm.XhmmMergeGatkDepths
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Config
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment