Merge branch 'develop' into feature-FilterOnMappingQualityCarp

# Conflicts:
#	public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

@@ -153,11 +153,11 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
           scriptOutput.rawVcfFile = m2v.output
 
           val vcfFilter = new VcfFilter(this) {
-            override def defaults = ConfigUtils.mergeMaps(Map("min_sample_depth" -> 8,
+            override def defaults = Map("min_sample_depth" -> 8,
               "min_alternate_depth" -> 2,
               "min_samples_pass" -> 1,
               "filter_ref_calls" -> true
-            ), super.defaults)
+            )
           }
           vcfFilter.inputVcf = m2v.output
           vcfFilter.outputVcf = swapExt(outputDir, m2v.output, ".vcf", ".filter.vcf.gz")

public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala

@@ -35,10 +35,10 @@ trait BastyTrait extends MultiSampleQScript {
 
   def variantcallers = List("freebayes")
 
-  override def defaults = ConfigUtils.mergeMaps(Map(
+  override def defaults = Map(
     "ploidy" -> 1,
     "variantcallers" -> variantcallers
-  ), super.defaults)
+  )
 
   lazy val shiva: ShivaTrait = new Shiva(qscript)
 

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala

@@ -47,7 +47,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction with Refe
   override def defaultCoreMemory = 4.0
   override def defaultThreads = 8
 
-  var sam: Boolean = config("sam", default = true)
+  var sam: Boolean = config("sam", default = false)
   var sam_RG: Option[String] = config("sam-RG")
   var seedlen: Option[Int] = config("seedlen")
   var seedmms: Option[Int] = config("seedmms")

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala

@@ -53,6 +53,8 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
   @Argument(doc = "IS_BISULFITE_SEQUENCED", required = false)
   var isBisulfiteSequinced: Option[Boolean] = config("isbisulfitesequinced")
 
+  override def defaultCoreMemory = 8.0
+
   override def beforeGraph() {
     super.beforeGraph()
     if (outputChart == null) outputChart = new File(output + ".pdf")

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala

@@ -33,7 +33,7 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard with Summari
 
   javaMainClass = new picard.analysis.CollectMultipleMetrics().getClass.getName
 
-  override def defaultCoreMemory = 6.0
+  override def defaultCoreMemory = 8.0
 
   @Input(doc = "The input SAM or BAM files to analyze", required = true)
   var input: File = null

public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala

@@ -25,17 +25,10 @@ import scala.sys.process.{ Process, ProcessLogger }
 
 class GsnapTest extends TestNGSuite with Matchers {
 
-  private def setConfig(key: String, value: String): Map[String, Any] = {
-    val oldMap: Map[String, Any] = Config.global.map
-    Config.global.map += (key -> value)
-    oldMap
-  }
-
-  private def restoreConfig(oldMap: Map[String, Any]): Unit = Config.global.map = oldMap
-
   @BeforeClass def checkExecutable() = {
-    val oldMap = setConfig("db", "mock")
-    val wrapper = new Gsnap(null)
+    val wrapper = new Gsnap(null) {
+      override def globalConfig = new Config(Map("db" -> "mock"))
+    }
     val proc = Process(wrapper.versionCommand)
     val exitCode =
       try {
@@ -47,13 +40,12 @@ class GsnapTest extends TestNGSuite with Matchers {
       }
     if (exitCode != 0)
       throw new SkipException("Skipping GSNAP test because the executable can not be found")
-    restoreConfig(oldMap)
   }
 
   @Test(description = "GSNAP version number capture from executable")
   def testVersion() = {
-    val oldMap = setConfig("db", "mock")
-    new Gsnap(null).getVersion should not be "N/A"
-    restoreConfig(oldMap)
+    new Gsnap(null) {
+      override def globalConfig = new Config(Map("db" -> "mock"))
+    }.getVersion should not be "N/A"
   }
 }

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

@@ -21,11 +21,11 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils._
 
 /**
  * This class can store nested config values
- * @param map Map with value for new config
+ * @param _map Map with value for new config
  * @constructor Load config with existing map
  */
-class Config(var map: Map[String, Any],
-             protected[config] var defaults: Map[String, Any] = Map()) extends Logging {
+class Config(protected var _map: Map[String, Any],
+             protected var _defaults: Map[String, Any] = Map()) extends Logging {
   logger.debug("Init phase of config")
 
   /** Default constructor */
@@ -34,6 +34,9 @@ class Config(var map: Map[String, Any],
     loadDefaultConfig()
   }
 
+  def map = _map
+  def defaults = _defaults
+
   /**
    * Loading a environmental variable as location of config files to merge into the config
    * @param valueName Name of value
@@ -65,13 +68,13 @@ class Config(var map: Map[String, Any],
   def loadConfigFile(configFile: File, default: Boolean = false) {
     val configMap = fileToConfigMap(configFile)
     if (default) {
-      if (defaults.isEmpty) defaults = configMap
-      else defaults = mergeMaps(configMap, defaults)
-      logger.debug("New defaults: " + defaults)
+      if (_defaults.isEmpty) _defaults = configMap
+      else _defaults = mergeMaps(configMap, _defaults)
+      logger.debug("New defaults: " + _defaults)
     } else {
-      if (map.isEmpty) map = configMap
-      else map = mergeMaps(configMap, map)
-      logger.debug("New config: " + map)
+      if (_map.isEmpty) _map = configMap
+      else _map = mergeMaps(configMap, _map)
+      logger.debug("New config: " + _map)
     }
   }
 
@@ -84,11 +87,12 @@ class Config(var map: Map[String, Any],
    */
   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)
+    if (default) _defaults = mergeMaps(valueMap, _defaults)
+    else _map = mergeMaps(valueMap, _map)
   }
 
   protected[config] var notFoundCache: List[ConfigValueIndex] = List()
+  protected[config] var fixedCache: Map[ConfigValueIndex, ConfigValue] = Map()
   protected[config] var foundCache: Map[ConfigValueIndex, ConfigValue] = Map()
   protected[config] var defaultCache: Map[ConfigValueIndex, ConfigValue] = Map()
   protected[config] def clearCache(): Unit = {
@@ -103,24 +107,39 @@ class Config(var map: Map[String, Any],
    * @param s key
    * @return True if exist
    */
-  def contains(s: String): Boolean = map.contains(s)
+  def contains(s: String): Boolean = _map.contains(s)
+
+  /**
+   * Checks if value exist in config
+   * @param requestedIndex Index to value
+   * @return True if exist
+   */
+  def contains(requestedIndex: ConfigValueIndex): Boolean = contains(requestedIndex, Map())
 
   /**
    * Checks if value exist in config
    * @param requestedIndex Index to value
+   * @param fixedValues Fixed values
    * @return True if exist
    */
-  def contains(requestedIndex: ConfigValueIndex): Boolean =
+  def contains(requestedIndex: ConfigValueIndex, fixedValues: Map[String, Any]): Boolean =
     if (notFoundCache.contains(requestedIndex)) false
+    else if (fixedCache.contains(requestedIndex)) true
     else if (foundCache.contains(requestedIndex)) true
     else {
-      val value = Config.getValueFromMap(map, requestedIndex)
-      if (value.isDefined && value.get.value != None) {
-        foundCache += (requestedIndex -> value.get)
+      val fixedValue = Config.getValueFromMap(fixedValues, requestedIndex)
+      if (fixedValue.isDefined) {
+        fixedCache += (requestedIndex -> fixedValue.get)
         true
       } else {
-        notFoundCache +:= requestedIndex
-        false
+        val value = Config.getValueFromMap(_map, requestedIndex)
+        if (value.isDefined && value.get.value != None) {
+          foundCache += (requestedIndex -> value.get)
+          true
+        } else {
+          notFoundCache +:= requestedIndex
+          false
+        }
       }
     }
 
@@ -132,9 +151,12 @@ class Config(var map: Map[String, Any],
    * @param freeVar Default true, if set false value must exist in module
    * @return True if exist
    */
-  def contains(module: String, path: List[String], key: String, freeVar: Boolean = true): Boolean = {
+  def contains(module: String, path: List[String],
+               key: String,
+               freeVar: Boolean = true,
+               fixedValues: Map[String, Any] = Map()): Boolean = {
     val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
-    contains(requestedIndex)
+    contains(requestedIndex, fixedValues)
   }
 
   /**
@@ -146,10 +168,23 @@ class Config(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): ConfigValue = {
+  protected[config] 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)) foundCache(requestedIndex)
-    else if (default != null) {
+    if (contains(requestedIndex, fixedValues)) {
+      val fixedValue = fixedCache.get(requestedIndex)
+      if (fixedValue.isDefined) {
+        val userValue = Config.getValueFromMap(_map, requestedIndex)
+        if (userValue.isDefined)
+          logger.warn(s"Ignoring user-supplied value ${requestedIndex.key} at path ${requestedIndex.path} because it is a fixed value.")
+      }
+
+      fixedValue.getOrElse(foundCache(requestedIndex))
+    } else if (default != null) {
       defaultCache += (requestedIndex -> ConfigValue(requestedIndex, null, default, freeVar))
       defaultCache(requestedIndex)
     } else ConfigValue(requestedIndex, null, null, freeVar)
@@ -179,9 +214,11 @@ class Config(var map: Map[String, Any],
 
     // Positions where values are found
     val found = convertIndexValuesToMap(foundCache.filter(!_._2.default).toList.map(x => (x._2.foundIndex, x._2.value)))
+    val fixed = convertIndexValuesToMap(fixedCache.filter(!_._2.default).toList.map(x => (x._2.foundIndex, x._2.value)))
 
     // Positions where to start searching
     val effectiveFound = convertIndexValuesToMap(foundCache.filter(!_._2.default).toList.map(x => (x._2.requestIndex, x._2.value)), Some(false))
+    val effectiveFixed = convertIndexValuesToMap(fixedCache.filter(!_._2.default).toList.map(x => (x._2.requestIndex, x._2.value)), Some(false))
     val effectiveDefaultFound = convertIndexValuesToMap(defaultCache.filter(_._2.default).toList.map(x => (x._2.requestIndex, x._2.value)), Some(false))
     val notFound = convertIndexValuesToMap(notFoundCache.map((_, None)), Some(false))
 
@@ -189,16 +226,19 @@ class Config(var map: Map[String, Any],
     val fullEffective = ConfigUtils.mergeMaps(effectiveFound, effectiveDefaultFound)
     val fullEffectiveWithNotFound = ConfigUtils.mergeMaps(fullEffective, notFound)
 
-    writeMapToJsonFile(this.map, "input")
+    writeMapToJsonFile(_map, "input")
+    writeMapToJsonFile(_defaults, "defaults")
     writeMapToJsonFile(found, "found")
+    writeMapToJsonFile(fixed, "fixed")
     writeMapToJsonFile(effectiveFound, "effective.found")
+    writeMapToJsonFile(effectiveFixed, "effective.fixed")
     writeMapToJsonFile(effectiveDefaultFound, "effective.defaults")
     writeMapToJsonFile(notFound, "not.found")
     writeMapToJsonFile(fullEffective, "effective.full")
     writeMapToJsonFile(fullEffectiveWithNotFound, "effective.full.notfound")
   }
 
-  override def toString: String = map.toString()
+  override def toString: String = _map.toString()
 }
 
 object Config extends Logging {
@@ -210,7 +250,7 @@ object Config extends Logging {
    * @param config2 Low prio map
    * @return Merged config
    */
-  def mergeConfigs(config1: Config, config2: Config): Config = new Config(mergeMaps(config1.map, config2.map))
+  def mergeConfigs(config1: Config, config2: Config): Config = new Config(mergeMaps(config1._map, config2._map))
 
   /**
    * Search for value in index position in a map

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

@@ -15,6 +15,7 @@
  */
 package nl.lumc.sasc.biopet.utils.config
 
+import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
 
 trait Configurable extends ImplicitConversions {
@@ -35,9 +36,28 @@ trait Configurable extends ImplicitConversions {
   def configFullPath: List[String] = configPath ::: configName :: Nil
 
   /** Map to store defaults for config */
-  def defaults: Map[String, Any] = {
-    if (root != null) root.defaults
-    else globalConfig.defaults
+  def defaults: Map[String, Any] = Map()
+
+  /** This method merge defaults from the root to it's own */
+  protected def internalDefaults: Map[String, Any] = {
+    (root != null, defaults.isEmpty) match {
+      case (true, true)   => root.defaults
+      case (true, false)  => ConfigUtils.mergeMaps(defaults, root.defaults)
+      case (false, true)  => globalConfig.defaults
+      case (false, false) => ConfigUtils.mergeMaps(defaults, globalConfig.defaults)
+    }
+  }
+
+  /** All values found in this map will be skipped from the user config */
+  def fixedValues: Map[String, Any] = Map()
+
+  /** This method merge fixedValues from the root to it's own */
+  protected def internalFixedValues: Map[String, Any] = {
+    (root != null, fixedValues.isEmpty) match {
+      case (true, true)  => root.internalFixedValues
+      case (true, false) => ConfigUtils.mergeMaps(fixedValues, root.internalFixedValues)
+      case _             => fixedValues
+    }
   }
 
   val config = new ConfigFunctions
@@ -90,11 +110,11 @@ trait Configurable extends ImplicitConversions {
       val m = if (submodule != null) submodule else configName
       val p = if (path == null) getConfigPath(s, l, submodule) ::: subPath else path
       val d = {
-        val value = Config.getValueFromMap(defaults, ConfigValueIndex(m, p, key, freeVar))
+        val value = Config.getValueFromMap(internalDefaults, ConfigValueIndex(m, p, key, freeVar))
         if (value.isDefined) value.get.value else default
       }
-      if (d == null) globalConfig(m, p, key, freeVar = freeVar)
-      else globalConfig(m, p, key, d, freeVar)
+      if (d == null) globalConfig(m, p, key, freeVar = freeVar, fixedValues = internalFixedValues)
+      else globalConfig(m, p, key, d, freeVar, fixedValues = internalFixedValues)
     }
 
     /**
@@ -117,7 +137,7 @@ trait Configurable extends ImplicitConversions {
       val m = if (submodule != null) submodule else configName
       val p = if (path == null) getConfigPath(s, l, submodule) ::: subPath else path
 
-      globalConfig.contains(m, p, key, freeVar) || Config.getValueFromMap(defaults, ConfigValueIndex(m, p, key, freeVar)).isDefined
+      globalConfig.contains(m, p, key, freeVar, internalFixedValues) || Config.getValueFromMap(internalDefaults, ConfigValueIndex(m, p, key, freeVar)).isDefined
     }
   }
 }

public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala

@@ -25,10 +25,36 @@ import org.testng.annotations.Test
  * Created by pjvan_thof on 1/8/15.
  */
 class ConfigurableTest extends TestNGSuite with Matchers {
+
+  abstract class Cfg extends Configurable {
+    def get(key: String,
+            default: String = null,
+            submodule: String = null,
+            freeVar: Boolean = true,
+            sample: String = null,
+            library: String = null) = {
+      config(key, default, submodule, freeVar = freeVar, sample = sample, library = library)
+    }
+  }
+
+  class ClassA(val root: Configurable) extends Cfg
+
+  class ClassB(val root: Configurable) extends Cfg {
+    lazy val classA = new ClassA(this)
+    // Why this needs to be lazy?
+  }
+
+  class ClassC(val root: Configurable) extends Cfg {
+    def this() = this(null)
+    lazy val classB = new ClassB(this)
+    // Why this needs to be lazy?
+  }
+
   @Test def testConfigurable(): Unit = {
     val classC = new ClassC {
       override def configName = "classc"
       override val globalConfig = new Config(ConfigurableTest.map)
+      override val fixedValues = Map("fixed" -> "fixed")
     }
 
     classC.configPath shouldBe Nil
@@ -51,46 +77,33 @@ class ConfigurableTest extends TestNGSuite with Matchers {
     classC.get("bla", sample = "sample1", library = "library1").asString shouldBe "bla"
     classC.get("test", sample = "sample1", library = "library1").asString shouldBe "test"
     classC.get("test", sample = "sample1").asString shouldBe "test"
-  }
-}
 
-abstract class Cfg extends Configurable {
-  def get(key: String,
-          default: String = null,
-          submodule: String = null,
-          freeVar: Boolean = true,
-          sample: String = null,
-          library: String = null) = {
-    config(key, default, submodule, freeVar = freeVar, sample = sample, library = library)
+    // Fixed values
+    classC.get("fixed").asString shouldBe "fixed"
+    classC.classB.get("fixed").asString shouldBe "fixed"
+    classC.classB.classA.get("fixed").asString shouldBe "fixed"
   }
 }
 
-class ClassA(val root: Configurable) extends Cfg
-
-class ClassB(val root: Configurable) extends Cfg {
-  lazy val classA = new ClassA(this)
-  // Why this needs to be lazy?
-}
-
-class ClassC(val root: Configurable) extends Cfg {
-  def this() = this(null)
-  lazy val classB = new ClassB(this)
-  // Why this needs to be lazy?
-}
-
 object ConfigurableTest {
   val map = Map(
+    "fixed" -> "nonfixed",
     "classa" -> Map(
-      "k1" -> "a1"
+      "k1" -> "a1",
+      "fixed" -> "nonfixed"
     ), "classb" -> Map(
-      "k1" -> "b1"
+      "k1" -> "b1",
+      "fixed" -> "nonfixed"
     ), "classc" -> Map(
-      "k1" -> "c1"
+      "k1" -> "c1",
+      "fixed" -> "nonfixed"
     ), "samples" -> Map(
       "sample1" -> Map(
+        "fixed" -> "nonfixed",
         "test" -> "test",
         "libraries" -> Map(
           "library1" -> Map(
+            "fixed" -> "nonfixed",
             "bla" -> "bla"
           )
         )

public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala

@@ -39,16 +39,14 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
   qscript =>
   def this() = this(null)
 
-  override def defaults = ConfigUtils.mergeMaps(Map(
+  override def defaults = Map(
     "mapping" -> Map(
       "skip_markduplicates" -> false,
       "aligner" -> "bwa-mem"
     ),
     "samtoolsview" -> Map("q" -> 10)
-  ), super.defaults)
-
-
-
+  )
+  
   def summaryFile = new File(outputDir, "Carp.summary.json")
 
   //TODO: Add summary

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala

@@ -201,7 +201,8 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
 
   def summaryStats: Map[String, Any] = Map(
     "per_base_sequence_quality" -> perBaseSequenceQuality,
-    "per_base_sequence_content" -> perBaseSequenceContent)
+    "per_base_sequence_content" -> perBaseSequenceContent,
+    "adapters" -> foundAdapters.map(x => x.name -> x.seq).toMap)
 }
 
 object Fastqc {

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala

@@ -250,24 +250,22 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
     if (fastq_R1.length != fastq_R2.length && paired)
       throw new IllegalStateException("R1 and R2 file number is not the same")
 
-    if (!skipTrim || !skipClip) {
-      if (fastq_R1.length > 1) {
-        add(Zcat(this, fastq_R1, fastqR1Qc) | new Gzip(this) > fastqR1Qc)
-        if (paired) add(Zcat(this, fastq_R2, fastqR2Qc.get) | new Gzip(this) > fastqR2Qc.get)
-      }
+    if (fastq_R1.length > 1) {
+      add(Zcat(this, fastq_R1, fastqR1Qc) | new Gzip(this) > fastqR1Qc)
+      if (paired) add(Zcat(this, fastq_R2, fastqR2Qc.get) | new Gzip(this) > fastqR2Qc.get)
+    }
 
-      outputFiles += ("output_R1_gzip" -> fastqR1Qc)
-      if (paired) outputFiles += ("output_R2_gzip" -> fastqR2Qc.get)
+    outputFiles += ("output_R1_gzip" -> fastqR1Qc)
+    if (paired) outputFiles += ("output_R2_gzip" -> fastqR2Qc.get)
 
-      fastqc_R1_after = Fastqc(this, fastqR1Qc, new File(outputDir, R1_name + ".qc.fastqc/"))
-      add(fastqc_R1_after)
-      addSummarizable(fastqc_R1_after, "fastqc_R1_qc")
+    fastqc_R1_after = Fastqc(this, fastqR1Qc, new File(outputDir, R1_name + ".qc.fastqc/"))
+    add(fastqc_R1_after)
+    addSummarizable(fastqc_R1_after, "fastqc_R1_qc")
 
-      if (paired) {
-        fastqc_R2_after = Fastqc(this, fastqR2Qc.get, new File(outputDir, R2_name + ".qc.fastqc/"))
-        add(fastqc_R2_after)
-        addSummarizable(fastqc_R2_after, "fastqc_R2_qc")
-      }
+    if (paired) {
+      fastqc_R2_after = Fastqc(this, fastqR2Qc.get, new File(outputDir, R2_name + ".qc.fastqc/"))
+      add(fastqc_R2_after)
+      addSummarizable(fastqc_R2_after, "fastqc_R2_qc")
     }
 
     addSummaryJobs()

public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala

@@ -73,11 +73,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
     flexiprep.libId = Some("1")
     flexiprep.script()
 
-    flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe (
-      if (paired && (skipClip && skipTrim)) 2
-      else if (!paired && (skipClip && skipTrim)) 1
-      else if (paired && !(skipClip && skipTrim)) 4
-      else if (!paired && !(skipClip && skipTrim)) 2)
+    flexiprep.functions.count(_.isInstanceOf[Fastqc]) shouldBe (if (paired) 4 else 2)
     flexiprep.functions.count(_.isInstanceOf[SeqStat]) shouldBe (if (paired) 4 else 2)
   }
 

public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala

@@ -100,24 +100,23 @@ class Gentrap(val root: Configurable) extends QScript
     })
 
   /** Default pipeline config */
-  override def defaults = ConfigUtils.mergeMaps(
-    Map(
-      "gsnap" -> Map(
-        "novelsplicing" -> 1,
-        "batch" -> 4,
-        "format" -> "sam"
-      ),
-      "cutadapt" -> Map("minimum_length" -> 20),
-      // avoid conflicts when merging since the MarkDuplicate tags often cause merges to fail
-      "picard" -> Map(
-        "programrecordid" -> "null"
-      ),
-      // disable markduplicates since it may not play well with all aligners (this can still be overriden via config)
-      "mapping" -> Map(
-        "skip_markduplicates" -> true,
-        "skip_metrics" -> true
-      )
-    ), super.defaults)