Added commandline support for config

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

@@ -30,9 +30,12 @@ import scala.collection.mutable.ListBuffer
  */
 trait BiopetQScript extends Configurable with GatkLogging {
 
-  @Argument(doc = "JSON config file(s)", fullName = "config_file", shortName = "config", required = false)
+  @Argument(doc = "JSON / YAML config file(s)", fullName = "config_file", shortName = "config", required = false)
   val configfiles: List[File] = Nil
 
+  @Argument(doc = "JSON config file(s)", fullName = "config_value", shortName = "cv", required = false)
+  val configValues: List[String] = Nil
+
   var outputDir: File = {
     Config.getValueFromMap(globalConfig.map, ConfigValueIndex(this.configName, configPath, "output_dir")) match {
       case Some(value) => new File(value.asString).getAbsoluteFile
@@ -61,7 +64,11 @@ trait BiopetQScript extends Configurable with GatkLogging {
    * Script from queue itself, final to force some checks for each pipeline and write report
    */
   final def script() {
-    outputDir = config("output_dir").asFile.getAbsoluteFile
+    if (config.contains("output_dir")) outputDir = config("output_dir").asFile.getAbsoluteFile
+    else {
+      outputDir = new File(".").getAbsoluteFile
+      BiopetQScript.addError("No output_dir defined in config")
+    }
     init
     biopetScript
 

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

@@ -42,6 +42,17 @@ trait PipelineCommand extends MainCommand with GatkLogging {
         if (t >= argsSize) throw new IllegalStateException("-config needs a value")
         Config.global.loadConfigFile(new File(args(t + 1)))
       }
+
+      if (args(t) == "-cv" || args(t) == "--config_value") {
+        val v = args(t + 1).split("=")
+        require(v.size == 2, "Value should be formatted like 'key=value' or 'path:path:key=value'")
+        val value = v(1)
+        val p = v(0).split(":")
+        val key = p.last
+        val path = p.dropRight(1).toList
+        Config.global.addValue(key, value, path)
+      }
+
       if (args(t) == "--logging_level" || args(t) == "-l") {
         args(t + 1).toLowerCase match {
           case "debug" => Logging.logger.setLevel(org.apache.log4j.Level.DEBUG)

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

@@ -79,6 +79,19 @@ class Config(var map: Map[String, Any],
     }
   }
 
+  /**
+   * Add a single vallue to the config
+   * @param key key of value
+   * @param value value itself
+   * @param path Path to value
+   * @param default if true value is put in default map
+   */
+  def addValue(key: String, value: Any, path: List[String] = Nil, default: Boolean = false): Unit = {
+    val valueMap = path.foldRight(Map(key -> value))((a, b) => Map(a -> b))
+    if (default) defaults = mergeMaps(valueMap, defaults)
+    else map = mergeMaps(valueMap, map)
+  }
+
   protected[config] var notFoundCache: List[ConfigValueIndex] = List()
   protected[config] var foundCache: Map[ConfigValueIndex, ConfigValue] = Map()
   protected[config] var defaultCache: Map[ConfigValueIndex, ConfigValue] = Map()