no more failing tests :-)

docs/developer/example-pipeline.md

@@ -138,7 +138,7 @@ Setting up the pipeline is done within the pipeline itself, fine-tuning is alway
 
 For our new pipeline, one should setup the (default) config options.
 
-Since our pipeline is called `HelloPipeline`, the root of the configNamespace for our pipeline will be called `hellopipeline` (lowercaps).
+Since our pipeline is called `HelloPipeline`, the root of the namespace for our pipeline will be called `hellopipeline` (lowercaps).
 
 ```json
 {

docs/pipelines/basty.md

@@ -34,7 +34,7 @@ Please refer [to our mapping pipeline](mapping.md) for information about how the
 
 #### Required configuration values
 
-| configNamespace | Name | Type | Default | Function |
+| namespace | Name | Type | Default | Function |
 | --------- | ---- | ---- | ------- | -------- |
 | shiva | variantcallers | List[String] |  | Which variant caller to use |
 | - | output_dir | Path | Path to output directory |
@@ -44,7 +44,7 @@ Please refer [to our mapping pipeline](mapping.md) for information about how the
 
 Specific configuration options additional to Basty are:
 
-| configNamespace | Name | Type | Default | Function |
+| namespace | Name | Type | Default | Function |
 | --------- | ---- | ---- | ------- | -------- |
 | raxml | seed | Integer | 12345 | RAxML Random seed|
 | raxml | raxml_ml_model | String | GTRGAMMAX | RAxML model |

docs/pipelines/shiva.md

@@ -161,7 +161,7 @@ The other mode, `library_variantcalling`, will call simultaneously call all libr
 
 The config for these therefore is:
 
-| configNamespace | Name | Type | Default | Function |
+| namespace | Name | Type | Default | Function |
 | ----------- | ---- | ---- | ------- | -------- |
 | shiva | multisample_variantcalling | Boolean | true | Default, multisample calling |
 | shiva | single_sample_variantcalling | Boolean | false | Not-recommended, single sample, merged bam |

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

@@ -20,7 +20,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
   qscript =>
   def this() = this(null)
 
-  /** Make variantcalling configNamespace, this with the gatk modes in there */
+  /** Make variantcalling namespace, this with the gatk modes in there */
   override def makeVariantcalling(multisample: Boolean = false) = {
     if (multisample) new ShivaVariantcalling(qscript) {
       override def namePrefix = "multisample"

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

@@ -131,11 +131,11 @@ trait BastyTrait extends MultiSampleQScript {
       raxmlMl.p = Some(seed)
       raxmlMl.n = outputName + "_ml"
       raxmlMl.w = dirSufixRaxml
-      raxmlMl.N = config("ml_runs", default = 20, configNamespace = "raxml")
+      raxmlMl.N = config("ml_runs", default = 20, namespace = "raxml")
       add(raxmlMl)
 
       val r = new scala.util.Random(seed)
-      val numBoot = config("boot_runs", default = 100, configNamespace = "raxml").asInt
+      val numBoot = config("boot_runs", default = 100, namespace = "raxml").asInt
       val bootList = for (t <- 0 until numBoot) yield {
         val raxmlBoot = new Raxml(this)
         raxmlBoot.input = variants

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

@@ -19,7 +19,7 @@ import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
 
 /** Biopet commandline class for java based programs */
 trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunction {
-  executable = config("java", default = "java", configNamespace = "java", freeVar = false)
+  executable = config("java", default = "java", namespace = "java", freeVar = false)
 
   javaGCThreads = config("java_gc_threads", default = 4)
   javaGCHeapFreeLimit = config("java_gc_heap_freelimit", default = 10)

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

@@ -31,7 +31,7 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
   @Argument(doc = "JSON / YAML config file(s)", fullName = "config_file", shortName = "config", required = false)
   val configfiles: List[File] = Nil
 
-  @Argument(doc = "Config values, value should be formatted like 'key=value' or 'configNamespace:configNamespace:key=value'", fullName = "config_value", shortName = "cv", required = false)
+  @Argument(doc = "Config values, value should be formatted like 'key=value' or 'namespace:namespace:key=value'", fullName = "config_value", shortName = "cv", required = false)
   val configValues: List[String] = Nil
 
   /** Output directory of pipeline */

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

@@ -70,7 +70,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
       def libDir = new File(sampleDir, "lib_" + libId)
 
       lazy val libTags: Map[String, Any] =
-        config("tags", default = Map(), freeVar = false, configNamespace = libId, path = List("samples", sampleId, "libraries"))
+        config("tags", default = Map(), freeVar = false, namespace = libId, path = List("samples", sampleId, "libraries"))
 
       def sampleId = sample.sampleId
 
@@ -91,7 +91,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
     val libraries: Map[String, Library] = libIds.map(id => id -> makeLibrary(id)).toMap
 
     lazy val sampleTags: Map[String, Any] =
-      config("tags", default = Map(), freeVar = false, configNamespace = sampleId, path = List("samples"))
+      config("tags", default = Map(), freeVar = false, namespace = sampleId, path = List("samples"))
 
     lazy val gender = {
       val g: Option[String] = sampleTags.get("gender").map(_.toString)

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

@@ -24,7 +24,7 @@ trait PythonCommandLineFunction extends BiopetCommandLineFunction {
   @Input(doc = "Python script", required = false)
   var pythonScript: File = _
 
-  executable = config("exe", default = "python", configNamespace = "python", freeVar = false)
+  executable = config("exe", default = "python", namespace = "python", freeVar = false)
 
   protected var pythonScriptName: String = _
 

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

@@ -40,7 +40,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction with Vers
   var output: File = null
 
   executable = config("exe", default = "fastqc")
-  var javaExe: String = config("exe", default = "java", configNamespace = "java", freeVar = false)
+  var javaExe: String = config("exe", default = "java", namespace = "java", freeVar = false)
   var kmers: Option[Int] = config("kmers")
   var quiet: Boolean = config("quiet", default = false)
   var noextract: Boolean = config("noextract", default = false)

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

@@ -32,7 +32,7 @@ import scala.io.Source
  */
 class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version with Summarizable {
 
-  executable = config("exe", configNamespace = "perl", default = "perl")
+  executable = config("exe", namespace = "perl", default = "perl")
   var vepScript: String = config("vep_script")
 
   @Input(doc = "input VCF", required = true)

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

@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 
 abstract class Bcftools extends BiopetCommandLineFunction with Version {
   override def subPath = "bcftools" :: super.subPath
-  executable = config("exe", default = "bcftools", configNamespace = "bcftools", freeVar = false)
+  executable = config("exe", default = "bcftools", namespace = "bcftools", freeVar = false)
   def versionCommand = executable
   def versionRegex = """Version: (.*)""".r
   override def versionExitcode = List(0, 1)

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

@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 /** General abstract class for bedtools extensions */
 abstract class Bedtools extends BiopetCommandLineFunction with Version {
   override def subPath = "bedtools" :: super.subPath
-  executable = config("exe", default = "bedtools", configNamespace = "bedtools")
+  executable = config("exe", default = "bedtools", namespace = "bedtools")
   def versionCommand = executable + " --version"
   def versionRegex = """bedtools (.*)""".r
 }
\ No newline at end of file

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala

@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.engine.phonehome.GATKRunReport
 import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
 
 trait GatkGeneral extends CommandLineGATK with CommandLineResources with Reference with Version {
-  var executable: String = config("java", default = "java", configNamespace = "java", freeVar = false)
+  var executable: String = config("java", default = "java", namespace = "java", freeVar = false)
 
   override def subPath = "gatk" :: super.subPath
 

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

@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
  * Created by wyleung on 5-1-15
  */
 abstract class IGVTools extends BiopetCommandLineFunction with Version {
-  executable = config("exe", default = "igvtools", configNamespace = "igvtools", freeVar = false)
+  executable = config("exe", default = "igvtools", namespace = "igvtools", freeVar = false)
   def versionCommand = executable + " version"
   def versionRegex = """IGV Version:? ([\w\.]*) .*""".r
   override def versionExitcode = List(0)

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala

@@ -23,7 +23,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
  * Created by sajvanderzeeuw on 12/19/14.
  */
 abstract class Macs2 extends BiopetCommandLineFunction with Version {
-  executable = config("exe", default = "macs2", configNamespace = "macs2", freeVar = false)
+  executable = config("exe", default = "macs2", namespace = "macs2", freeVar = false)
   def versionCommand = executable + " --version"
   def versionRegex = """macs2 (.*)""".r
   override def versionExitcode = List(0, 1)

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

@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Argument }
  * manwe [subcommand]
  */
 abstract class Manwe extends BiopetCommandLineFunction {
-  executable = config("exe", default = "manwe", configNamespace = "manwe")
+  executable = config("exe", default = "manwe", namespace = "manwe")
 
   var manweConfig: File = createManweConfig(None)
 

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

@@ -24,7 +24,7 @@ abstract class Sambamba extends BiopetCommandLineFunction with Version {
 
   override def subPath = "sambamba" :: super.subPath
 
-  executable = config("exe", default = "sambamba", configNamespace = "sambamba", freeVar = false)
+  executable = config("exe", default = "sambamba", namespace = "sambamba", freeVar = false)
   def versionCommand = executable
   def versionRegex = """sambamba v(.*)""".r
   override def versionExitcode = List(0, 1)

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

@@ -20,7 +20,7 @@ import nl.lumc.sasc.biopet.core.{ Version, BiopetCommandLineFunction }
 /** General class for samtools extensions */
 abstract class Samtools extends BiopetCommandLineFunction with Version {
   override def subPath = "samtools" :: super.subPath
-  executable = config("exe", default = "samtools", configNamespace = "samtools", freeVar = false)
+  executable = config("exe", default = "samtools", namespace = "samtools", freeVar = false)
   def versionCommand = executable
   def versionRegex = """Version: (.*)""".r
   override def versionExitcode = List(0, 1)

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

@@ -319,7 +319,7 @@ object ConfigUtils extends Logging {
       val exist = valueExists(value)
       if (!exist)
         Logging.addError("Value does not exist but is required, key: " + value.requestIndex.key +
-          "  configNamespace: " + value.requestIndex.module,
+          "  namespace: " + value.requestIndex.module,
           if (value.requestIndex.path != Nil) "  path: " + value.requestIndex.path.mkString("->") else null)
       exist
     }

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

@@ -92,7 +92,7 @@ trait Configurable extends ImplicitConversions {
      *
      * @param key Name of value
      * @param default Default value if not found
-     * @param configNamespace Adds to the path
+     * @param namespace Adds to the path
      * @param freeVar Default true, if set false value must exist in module
      * @param sample Default null, when set path is prefixed with "samples" -> "sampleID"
      * @param library Default null, when set path is prefixed with "libraries" -> "libraryID"
@@ -100,15 +100,15 @@ trait Configurable extends ImplicitConversions {
      */
     def apply(key: String,
               default: Any = null,
-              configNamespace: String = null,
+              namespace: String = null,
               freeVar: Boolean = true,
               sample: String = null,
               library: String = null,
               path: List[String] = null): ConfigValue = {
       val s = if (sample != null || defaultSample.isEmpty) sample else defaultSample.get
       val l = if (library != null || defaultLibrary.isEmpty) library else defaultLibrary.get
-      val m = if (configNamespace != null) configNamespace else configNamespace
-      val p = if (path == null) getConfigPath(s, l, configNamespace) ::: subPath else path
+      val m = if (namespace != null) namespace else configNamespace
+      val p = if (path == null) getConfigPath(s, l, namespace) ::: subPath else path
       val d = {
         val value = Config.getValueFromMap(internalDefaults, ConfigValueIndex(m, p, key, freeVar))
         if (value.isDefined) value.get.value else default
@@ -120,22 +120,22 @@ trait Configurable extends ImplicitConversions {
     /**
      * Check if value exist in config
      * @param key Name of value
-     * @param configNamespace Adds to the path
+     * @param namespace Adds to the path
      * @param freeVar Default true, if set false value must exist in module
      * @param sample Default null, when set path is prefixed with "samples" -> "sampleID"
      * @param library Default null, when set path is prefixed with "libraries" -> "libraryID"
      * @return true when value is found in config
      */
     def contains(key: String,
-                 configNamespace: String = null,
+                 namespace: String = null,
                  freeVar: Boolean = true,
                  sample: String = null,
                  library: String = null,
                  path: List[String] = null) = {
       val s = if (sample != null || defaultSample.isEmpty) sample else defaultSample.get
       val l = if (library != null || defaultLibrary.isEmpty) library else defaultLibrary.get
-      val m = if (configNamespace != null) configNamespace else configNamespace
-      val p = if (path == null) getConfigPath(s, l, configNamespace) ::: subPath else path
+      val m = if (namespace != null) namespace else configNamespace
+      val p = if (path == null) getConfigPath(s, l, namespace) ::: subPath else path
 
       globalConfig.contains(m, p, key, freeVar, internalFixedValues) || Config.getValueFromMap(internalDefaults, ConfigValueIndex(m, p, key, freeVar)).isDefined
     }

public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala

@@ -30,7 +30,7 @@ import scala.sys.process.{ Process, ProcessLogger }
 trait Rscript extends Configurable {
   protected var script: File
 
-  def rscriptExecutable: String = config("exe", default = "Rscript", configNamespace = "rscript")
+  def rscriptExecutable: String = config("exe", default = "Rscript", namespace = "rscript")
 
   /** This is the defaul implementation, to add arguments override this */
   def cmd: Seq[String] = Seq(rscriptExecutable, script.getAbsolutePath)

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

@@ -29,11 +29,11 @@ class ConfigurableTest extends TestNGSuite with Matchers {
   abstract class Cfg extends Configurable {
     def get(key: String,
             default: String = null,
-            submodule: String = null,
+            configNamespace: String = null,
             freeVar: Boolean = true,
             sample: String = null,
             library: String = null) = {
-      config(key, default, submodule, freeVar = freeVar, sample = sample, library = library)
+      config(key, default, configNamespace, freeVar = freeVar, sample = sample, library = library)
     }
   }
 

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala

@@ -36,7 +36,7 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
     Some(shiva)
   }
 
-  /** Method to make the variantcalling configNamespace of shiva */
+  /** Method to make the variantcalling namespace of shiva */
   def makeVariantcalling(multisample: Boolean = false): ShivaVariantcallingTrait with QScript = {
     if (multisample) new ShivaVariantcalling(qscript) {
       override def namePrefix = "multisample"

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala

@@ -92,8 +92,8 @@ trait ShivaVariantcallingTrait extends SummaryQScript
       caller.outputDir = new File(outputDir, caller.name)
       add(caller)
       addStats(caller.outputFile, caller.name)
-      val normalize: Boolean = config("execute_vt_normalize", default = false, configNamespace = caller.configNamespace)
-      val decompose: Boolean = config("execute_vt_decompose", default = false, configNamespace = caller.configNamespace)
+      val normalize: Boolean = config("execute_vt_normalize", default = false, namespace = caller.configNamespace)
+      val decompose: Boolean = config("execute_vt_decompose", default = false, namespace = caller.configNamespace)
 
       val vtNormalize = new VtNormalize(this)
       vtNormalize.inputVcf = caller.outputFile

public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala

@@ -119,8 +119,8 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
   def importAndActivateSample(sampleID: String, inputVcf: File,
                               gVCF: File, annotation: ManweAnnotateVcf): ManweActivateAfterAnnotImport = {
 
-    val minGQ: Int = config("minimum_genome_quality", default = 20, configNamespace = "manwe")
-    val isPublic: Boolean = config("varda_is_public", default = true, configNamespace = "manwe")
+    val minGQ: Int = config("minimum_genome_quality", default = 20, namespace = "manwe")
+    val isPublic: Boolean = config("varda_is_public", default = true, namespace = "manwe")
 
     val bedTrack = new GvcfToBed(this)
     bedTrack.inputVcf = gVCF
@@ -185,7 +185,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
    */
   def varda(vcf: File, gVcf: File): File = {
 
-    val annotationQueries: List[String] = config("annotation_queries", default = List("GLOBAL *"), configNamespace = "manwe")
+    val annotationQueries: List[String] = config("annotation_queries", default = List("GLOBAL *"), namespace = "manwe")
     //TODO: add groups!!! Need sample-specific group tags for this
 
     val annotate = new ManweAnnotateVcf(this)