Config report now happens in the background

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

@@ -24,6 +24,8 @@ import org.broadinstitute.gatk.queue.{ QScript, QSettings }
 import org.broadinstitute.gatk.queue.function.QFunction
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
 
+import scala.collection.mutable.ListBuffer
+
 /** Base for biopet pipeline */
 trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
 
@@ -95,6 +97,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
 
     logger.info("Running pre commands")
     var count = 0
+    val totalCount = functions.size
     for (function <- functions) {
       function match {
         case f: BiopetCommandLineFunction =>
@@ -106,15 +109,15 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
         case _               =>
       }
       count += 1
-      if (count % 500 == 0) logger.info(s"Preprocessing done for ${count} jobs out of ${functions.length} total")
+      if (count % 500 == 0) logger.info(s"Preprocessing done for $count jobs out of $totalCount total")
     }
-    logger.info(s"Preprocessing done for ${functions.length} functions")
+    logger.info(s"Preprocessing done for $totalCount functions")
 
     val logDir = new File(outputDir, ".log" + File.separator + qSettings.runName.toLowerCase)
 
     if (outputDir.getParentFile.canWrite || (outputDir.exists && outputDir.canWrite))
       globalConfig.writeReport(new File(logDir, "config"))
-    else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writeable, output directory cannot be created")
+    else Logging.addError("Parent of output dir: '" + outputDir.getParent + "' is not writable, output directory cannot be created")
 
     logger.info("Checking input files")
     inputFiles.par.foreach { i =>

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

@@ -14,11 +14,11 @@
  */
 package nl.lumc.sasc.biopet.core.summary
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 import java.sql.Date
 
 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.db.SummaryDb
 import org.broadinstitute.gatk.queue.QScript
 import nl.lumc.sasc.biopet.LastCommitHash

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala

@@ -15,9 +15,13 @@
 package nl.lumc.sasc.biopet.utils.config
 
 import java.io.{ File, PrintWriter }
-import nl.lumc.sasc.biopet.utils.{ Logging, ConfigUtils }
+
+import nl.lumc.sasc.biopet.utils.{ConfigUtils, Logging}
 import nl.lumc.sasc.biopet.utils.ConfigUtils._
 
+import scala.concurrent.Future
+import scala.concurrent.ExecutionContext.Implicits.global
+
 /**
  * This class can store nested config values
  * @param _map Map with value for new config
@@ -189,7 +193,7 @@ class Config(protected var _map: Map[String, Any],
     } else ConfigValue(requestedIndex, null, null, freeVar)
   }
 
-  def writeReport(directory: File): Unit = {
+  def writeReport(directory: File): Future[Unit] = Future {
     directory.mkdirs()
 
     def convertIndexValuesToMap(input: List[(ConfigValueIndex, Any)], forceFreeVar: Option[Boolean] = None): Map[String, Any] = {

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

@@ -6,8 +6,8 @@ import slick.driver.H2Driver.api._
 
 import scala.concurrent.ExecutionContext.Implicits.global
 import scala.concurrent.duration.Duration
-import scala.concurrent.{Await, Future}
-import java.io.{Closeable, File}
+import scala.concurrent.{ Await, Future }
+import java.io.{ Closeable, File }
 import java.sql.Date
 
 /**