Merge branch 'feature-auto_retry' into 'develop'

Added a default for the retry arg

Small option to add retry by default, also can use the config to set retries now

See merge request !264

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PipelineCommand.scala

@@ -18,13 +18,14 @@ package nl.lumc.sasc.biopet.core
 import java.io.{ File, PrintWriter }
 
 import nl.lumc.sasc.biopet.utils.config.Config
+import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
 import nl.lumc.sasc.biopet.core.workaround.BiopetQCommandLine
 import nl.lumc.sasc.biopet.utils.{ MainCommand, Logging }
 import org.apache.log4j.{ PatternLayout, WriterAppender }
 import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
 
 /** Wrapper around executable from Queue */
-trait PipelineCommand extends MainCommand with GatkLogging {
+trait PipelineCommand extends MainCommand with GatkLogging with ImplicitConversions {
 
   /**
    * Gets location of compiled class of pipeline
@@ -32,6 +33,8 @@ trait PipelineCommand extends MainCommand with GatkLogging {
    */
   def pipeline = "/" + getClass.getName.stripSuffix("$").replaceAll("\\.", "/") + ".class"
 
+  def pipelineName = getClass.getSimpleName.takeWhile(_ != '$').toLowerCase
+
   /** Class can be used directly from java with -cp option */
   def main(args: Array[String]): Unit = {
     val argsSize = args.length
@@ -87,6 +90,11 @@ trait PipelineCommand extends MainCommand with GatkLogging {
     if (!args.contains("--log_to_file") && !args.contains("-log")) {
       argv ++= List("--log_to_file", new File(logFile.getParentFile, "queue." + BiopetQCommandLine.timestamp + ".log").getAbsolutePath)
     }
+    if (!args.contains("-retry") && !args.contains("--retry_failed")) {
+      val retry: Int = Config.global(pipelineName, Nil, "retry", default = 5)
+      logger.info("No retry flag found, ")
+      argv ++= List("-retry", retry.toString)
+    }
     BiopetQCommandLine.main(argv)
   }
 }
\ No newline at end of file

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

@@ -168,12 +168,12 @@ class Config(protected var _map: Map[String, Any],
    * @param freeVar Default true, if set false value must exist in module
    * @return Config value
    */
-  protected[config] def apply(module: String,
-                              path: List[String],
-                              key: String,
-                              default: Any = null,
-                              freeVar: Boolean = true,
-                              fixedValues: Map[String, Any] = Map()): ConfigValue = {
+  def apply(module: String,
+            path: List[String],
+            key: String,
+            default: Any = null,
+            freeVar: Boolean = true,
+            fixedValues: Map[String, Any] = Map()): ConfigValue = {
     val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
     if (contains(requestedIndex, fixedValues)) {
       val fixedValue = fixedCache.get(requestedIndex)