Fix format

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.core
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
-import nl.lumc.sasc.biopet.core.summary.{Summarizable, SummaryQScript}
+import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
 import nl.lumc.sasc.biopet.utils.summary.SummaryDb
-import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
+import nl.lumc.sasc.biopet.utils.{ ConfigUtils, Logging }
 import org.broadinstitute.gatk.queue.QScript
 
 import scala.concurrent.Await

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala

@@ -112,9 +112,9 @@ object WriteDependencies extends Logging with Configurable {
           case cmd: CommandLineFunction => cmd.commandLine
           case _                        => None
         }), "main_job" -> (f match {
-          case cmd: BiopetCommandLineFunction            => cmd.mainFunction
+          case cmd: BiopetCommandLineFunction => cmd.mainFunction
           case s: WriteSummary if s.qscript.parent == null => true
-          case _                                         => false
+          case _ => false
         }), "intermediate" -> f.isIntermediate,
           "depends_on_intermediate" -> BiopetQScript.safeInputs(f).getOrElse(Seq()).exists(files(_).isIntermediate),
           "depends_on_jobs" -> BiopetQScript.safeInputs(f).getOrElse(Seq()).toList.flatMap(files(_).outputJobNames).distinct,

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala

@@ -14,10 +14,10 @@
  */
 package nl.lumc.sasc.biopet.core.summary
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.core._
-import nl.lumc.sasc.biopet.core.extensions.{CheckChecksum, Md5sum}
+import nl.lumc.sasc.biopet.core.extensions.{ CheckChecksum, Md5sum }
 import nl.lumc.sasc.biopet.utils.summary.SummaryDb
 import org.broadinstitute.gatk.queue.QScript
 
@@ -52,8 +52,8 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
   def summaryFile: File
 
   def summaryDbFile: File = root match {
-    case s:SummaryQScript => new File(s.outputDir, s"${s.summaryName}.summary.db")
-    case _ => throw new IllegalStateException("Root should be a SummaryQScript")
+    case s: SummaryQScript => new File(s.outputDir, s"${s.summaryName}.summary.db")
+    case _                 => throw new IllegalStateException("Root should be a SummaryQScript")
   }
 
   /**
@@ -113,10 +113,9 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
 
   private def runIdFile = root match {
     case s: SummaryQScript => new File(s.outputDir, s".log/summary.runid")
-    case _ => throw new IllegalStateException("Root should be a SummaryQscript")
+    case _                 => throw new IllegalStateException("Root should be a SummaryQscript")
   }
 
-
   private def createRun(): Int = {
     val db = SummaryDb.openSqliteSummary(summaryDbFile)
     val id = Await.result(db.createRun(summaryName, outputDir), Duration.Inf)

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala

@@ -14,15 +14,15 @@
  */
 package nl.lumc.sasc.biopet.core.summary
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.LastCommitHash
 import nl.lumc.sasc.biopet.utils.summary.SummaryDb
-import org.broadinstitute.gatk.queue.function.{InProcessFunction, QFunction}
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.queue.function.{ InProcessFunction, QFunction }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 import scala.collection.mutable
 import scala.io.Source
@@ -59,7 +59,7 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
     if (qscript == root) { // This initialize the database
       qscript match {
         case s: MultiSampleQScript => s.initSummaryDb
-        case _ => qscript.summaryRunId
+        case _                     => qscript.summaryRunId
       }
     }
     val db = SummaryDb.openSqliteSummary(qscript.summaryDbFile)
@@ -89,12 +89,12 @@ class WriteSummary(val parent: SummaryQScript) extends InProcessFunction with Co
 
     val pipelineId = Await.result(db.getPipelines(name = Some(qscript.summaryName), runId = Some(qscript.summaryRunId)).map(_.head.id), Duration.Inf)
 
-    for (((name, sampleName, libName), summarizables) <-qscript.summarizables) {
+    for (((name, sampleName, libName), summarizables) <- qscript.summarizables) {
       require(summarizables.nonEmpty)
       val stats = ConfigUtils.anyToJson(if (summarizables.size == 1) summarizables.head.summaryStats
       else {
         val s = summarizables.map(_.summaryStats)
-        s.tail.foldLeft(Map("stats" -> s.head))((a,b) =>
+        s.tail.foldLeft(Map("stats" -> s.head))((a, b) =>
           ConfigUtils.mergeMaps(a, Map("stats" -> b), summarizables.head.resolveSummaryConflict))("stats")
       })
       val moduleId = db.getModules(name = Some(name), runId = Some(qscript.summaryRunId), pipelineId = Some(pipelineId))

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToSqlite.scala

@@ -10,8 +10,8 @@ import scala.concurrent.Await
 import scala.concurrent.duration.Duration
 
 /**
-  * Created by pjvanthof on 26/01/2017.
-  */
+ * Created by pjvanthof on 26/01/2017.
+ */
 object SummaryToSqlite extends ToolCommand {
 
   case class Args(inputJson: File = null,
@@ -70,7 +70,7 @@ object SummaryToSqlite extends ToolCommand {
 
     println(Await.result(summary.getStats(runId = Some(runId), pipelineId = Some(pipelineId), sampleId = Option(None)), Duration.Inf))
 
-    println(Await.result(summary.getStat(0,0), Duration.Inf))
+    println(Await.result(summary.getStat(0, 0), Duration.Inf))
 
     db.close()
 

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryDb.scala

 package nl.lumc.sasc.biopet.utils.summary
 
-import java.io.{Closeable, File}
+import java.io.{ Closeable, File }
 
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import slick.driver.H2Driver.api._
 
-import scala.concurrent.{Await, Future}
+import scala.concurrent.{ Await, Future }
 import scala.concurrent.duration.Duration
 import nl.lumc.sasc.biopet.utils.summary.db.Schema._
 
 import scala.concurrent.ExecutionContext.Implicits.global
 
 /**
-  * Created by pjvanthof on 05/02/2017.
-  */
+ * Created by pjvanthof on 05/02/2017.
+ */
 class SummaryDb(db: Database) extends Closeable {
 
   def close(): Unit = db.close()
@@ -98,9 +98,10 @@ class SummaryDb(db: Database) extends Closeable {
 
   def createPipeline(name: String, runId: Int): Future[Int] = {
     getPipelines(name = Some(name), runId = Some(runId))
-      .flatMap{ case m =>
-        if (m.isEmpty) forceCreatePipeline(name, runId)
-        else Future(m.head.id)
+      .flatMap {
+        case m =>
+          if (m.isEmpty) forceCreatePipeline(name, runId)
+          else Future(m.head.id)
       }
   }
 
@@ -122,9 +123,10 @@ class SummaryDb(db: Database) extends Closeable {
 
   def createModule(name: String, runId: Int, pipelineId: Int): Future[Int] = {
     getModules(name = Some(name), runId = Some(runId), pipelineId = Some(pipelineId))
-      .flatMap{ case m =>
-        if (m.isEmpty) forceCreateModule(name, runId, pipelineId)
-        else Future(m.head.id)
+      .flatMap {
+        case m =>
+          if (m.isEmpty) forceCreateModule(name, runId, pipelineId)
+          else Future(m.head.id)
       }
   }
 
@@ -154,7 +156,7 @@ class SummaryDb(db: Database) extends Closeable {
   }
 
   private def statsFilter(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
-                           sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
+                          sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
     val l: List[Option[Query[Stats, Stats#TableElementType, Seq] => Query[Stats, Stats#TableElementType, Seq]]] = List(
       runId.map(x => y => y.filter(_.runId === x)),
       pipelineId.map(x => y => y.filter(_.pipelineId === x)),
@@ -162,7 +164,7 @@ class SummaryDb(db: Database) extends Closeable {
       sampleId.map(x => y => (if (x.isDefined) y.filter(_.sampleId === x) else y.filter(_.sampleId.isEmpty))),
       libId.map(x => y => (if (x.isDefined) y.filter(_.libraryId === x) else y.filter(_.libraryId.isEmpty)))
     )
-    l.flatten.foldLeft(stats.subquery)((a,b) => b(a))
+    l.flatten.foldLeft(stats.subquery)((a, b) => b(a))
   }
 
   def getStats(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
@@ -179,18 +181,18 @@ class SummaryDb(db: Database) extends Closeable {
       y => (if (sampleId.isDefined) y.filter(_.sampleId === sampleId) else y.filter(_.sampleId.isEmpty)),
       y => (if (libId.isDefined) y.filter(_.libraryId === libId) else y.filter(_.libraryId.isEmpty))
     )
-    val q = l.foldLeft(stats.subquery)((a,b) => b(a))
+    val q = l.foldLeft(stats.subquery)((a, b) => b(a))
 
     db.run(q.map(_.content).result).map(_.headOption.map(ConfigUtils.jsonTextToMap))
   }
 
   def createSetting(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,
-                 sampleId: Option[Int] = None, libId: Option[Int] = None, content: String) = {
+                    sampleId: Option[Int] = None, libId: Option[Int] = None, content: String) = {
     db.run(settings.forceInsert(Setting(runId, pipelineId, moduleId, sampleId, libId, content)))
   }
 
   def getSettings(runId: Option[Int] = None, pipelineId: Option[Int] = None, moduleId: Option[Option[Int]] = None,
-               sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
+                  sampleId: Option[Option[Int]] = None, libId: Option[Option[Int]] = None) = {
     val l: List[Option[Query[Settings, Settings#TableElementType, Seq] => Query[Settings, Settings#TableElementType, Seq]]] = List(
       runId.map(x => y => y.filter(_.runId === x)),
       pipelineId.map(x => y => y.filter(_.pipelineId === x)),
@@ -198,13 +200,13 @@ class SummaryDb(db: Database) extends Closeable {
       sampleId.map(x => y => (if (x.isDefined) y.filter(_.sampleId === x) else y.filter(_.sampleId.isEmpty))),
       libId.map(x => y => (if (x.isDefined) y.filter(_.libraryId === x) else y.filter(_.libraryId.isEmpty)))
     )
-    val q = l.flatten.foldLeft(settings.subquery)((a,b) => b(a))
+    val q = l.flatten.foldLeft(settings.subquery)((a, b) => b(a))
 
     db.run(q.result)
   }
 
   def getSetting(runId: Int, pipelineId: Int, moduleId: Option[Int] = None,
-              sampleId: Option[Int] = None, libId: Option[Int] = None): Future[Option[Map[String, Any]]] = {
+                 sampleId: Option[Int] = None, libId: Option[Int] = None): Future[Option[Map[String, Any]]] = {
     val l: List[Query[Settings, Settings#TableElementType, Seq] => Query[Settings, Settings#TableElementType, Seq]] = List(
       _.filter(_.runId === runId),
       _.filter(_.pipelineId === pipelineId),
@@ -213,7 +215,7 @@ class SummaryDb(db: Database) extends Closeable {
       y => (if (libId.isDefined) y.filter(_.libraryId === libId) else y.filter(_.libraryId.isEmpty))
     )
 
-    val q = l.foldLeft(settings.subquery)((a,b) => b(a))
+    val q = l.foldLeft(settings.subquery)((a, b) => b(a))
     db.run(q.map(_.content).result).map(_.headOption.map(ConfigUtils.jsonTextToMap))
   }
 }

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/Schema.scala

@@ -3,8 +3,8 @@ package nl.lumc.sasc.biopet.utils.summary.db
 import slick.driver.H2Driver.api._
 
 /**
-  * Created by pjvan_thof on 27-1-17.
-  */
+ * Created by pjvan_thof on 27-1-17.
+ */
 object Schema {
 
   case class Run(id: Int, name: String, outputDir: String)
@@ -118,7 +118,7 @@ object Schema {
   }
   val files = TableQuery[Files]
 
-  case class Executable(runId: Int, toolName: String, version : Option[String], javaVersion: Option[String], exeMd5: Option[String], javaMd5: Option[String])
+  case class Executable(runId: Int, toolName: String, version: Option[String], javaVersion: Option[String], exeMd5: Option[String], javaMd5: Option[String])
   class Executables(tag: Tag) extends Table[Executable](tag, "Executables") {
     def runId = column[Int]("runId")
     def toolName = column[String]("toolName")