Merge remote-tracking branch 'remotes/origin/develop' into feature-snp_test

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 configoptions will called `hellopipeline` (lowercaps).
+Since our pipeline is called `HelloPipeline`, the root of the namespace for our pipeline will be called `hellopipeline` (lowercaps).
 
 ```json
 {

docs/general/memory.md

@@ -20,7 +20,7 @@ We assume here that the cluster will amplify those values by the number of threa
 - **residentFactor**: 1.2
 - **vmemFactor**: 1.4, 2.0 for java jobs
 
-This are de defaults of biopet but each extension in biopet can set their own defaults. As example the *bwa mem* tools 
+This are the defaults of biopet but each extension in biopet can set their own defaults. As example the *bwa mem* tools 
 use by default 8 `threads` and `core_memory` of 6.0.
 
 ### Config

docs/pipelines/basty.md

@@ -34,7 +34,7 @@ Please refer [to our mapping pipeline](mapping.md) for information about how the
 
 #### Required configuration values
 
-| Submodule | 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:
 
-| Submodule | 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

@@ -105,7 +105,7 @@ To view all possible config options please navigate to our Gitlab wiki page
 <a href="https://git.lumc.nl/biopet/biopet/wikis/GATK-Variantcalling-Pipeline" target="_blank">Config</a>
 
 ### Required settings
-| Namespace | Name | Type | Default | Function |
+| Confignamespace | Name | Type | Default | Function |
 | ----------- | ---- | ---- | ------- | -------- |
 | - | output_dir | String |  | Path to output directory |
 | Shiva | variantcallers | List[String] | | Which variant callers to use |
@@ -113,7 +113,7 @@ To view all possible config options please navigate to our Gitlab wiki page
 
 ### Config options
 
-| Namespace | Name |  Type | Default | Function |
+| ConfignNamespace | Name |  Type | Default | Function |
 | ----------- | ---- | ----- | ------- | -------- |
 | shiva | species | String | unknown_species | Name of species, like H.sapiens |
 | shiva | reference_name | String | unknown_reference_name | Name of reference, like hg19 |
@@ -161,7 +161,7 @@ The other mode, `library_variantcalling`, will call simultaneously call all libr
 
 The config for these therefore is:
 
-| Namespace | 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-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala

@@ -26,7 +26,7 @@ class VariantRecalibrator(val root: Configurable) extends org.broadinstitute.gat
 object VariantRecalibrator {
   def apply(root: Configurable, input: File, recal_file: File, tranches_file: File, indel: Boolean = false): VariantRecalibrator = {
     val vr = new VariantRecalibrator(root) {
-      override lazy val configName = "variantrecalibrator"
+      override lazy val configNamespace = "variantrecalibrator"
       override def configPath: List[String] = (if (indel) "indel" else "snp") :: super.configPath
       if (indel) {
         mode = org.broadinstitute.gatk.tools.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL

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

@@ -20,15 +20,15 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
   qscript =>
   def this() = this(null)
 
-  /** Make variantcalling submodule, 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"
-      override def configName = "shivavariantcalling"
+      override def configNamespace = "shivavariantcalling"
       override def configPath: List[String] = super.configPath ::: "multisample" :: Nil
     }
     else new ShivaVariantcalling(qscript) {
-      override def configName = "shivavariantcalling"
+      override def configNamespace = "shivavariantcalling"
     }
   }
 

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala

@@ -27,7 +27,7 @@ import org.testng.annotations.{ DataProvider, Test }
 class ShivaTest extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): Shiva = {
     new Shiva() {
-      override def configName = "shiva"
+      override def configNamespace = "shiva"
       override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaTest.config))
       qSettings = new QSettings
       qSettings.runName = "test"

protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala

@@ -29,7 +29,7 @@ import scala.collection.mutable.ListBuffer
 class ShivaVariantcallingTest extends TestNGSuite with Matchers {
   def initPipeline(map: Map[String, Any]): ShivaVariantcalling = {
     new ShivaVariantcalling() {
-      override def configName = "shivavariantcalling"
+      override def configNamespace = "shivavariantcalling"
       override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaVariantcallingTest.config))
       qSettings = new QSettings
       qSettings.runName = "test"

public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -37,7 +37,7 @@ class BamMetricsTest extends TestNGSuite with Matchers {
 
   def initPipeline(map: Map[String, Any]): BamMetrics = {
     new BamMetrics() {
-      override def configName = "bammetrics"
+      override def configNamespace = "bammetrics"
       override def globalConfig = new Config(map)
       qSettings = new QSettings
       qSettings.runName = "test"

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, submodule = "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, submodule = "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/BiopetCommandLineFunction.scala

@@ -30,7 +30,7 @@ import scala.collection.JavaConversions._
 
 /** Biopet command line trait to auto check executable and cluster values */
 trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
-  analysisName = configName
+  analysisName = configNamespace
 
   @Input(doc = "deps", required = false)
   var deps: List[File] = Nil

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", submodule = "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/BiopetPipe.scala

@@ -74,7 +74,7 @@ class BiopetPipe(val commands: List[BiopetCommandLineFunction]) extends BiopetCo
   override def defaultThreads = 0
 
   val root: Configurable = commands.head.root
-  override def configName = commands.map(_.configName).mkString("-")
+  override def configNamespace = commands.map(_.configNamespace).mkString("-")
   def cmdLine: String = {
     "(" + commands.head.cmdLine + (if (commands.head.stdinFile.isDefined) {
       " < " + required(commands.head.stdinFile.map(_.getAbsoluteFile))

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 'path:path: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/CommandLineResources.scala

@@ -88,7 +88,7 @@ trait CommandLineResources extends CommandLineFunction with Configurable {
     else residentLimit = Some((_coreMemory + (0.5 * retryMultipler)) * residentFactor)
 
     if (!config.contains("vmem")) vmem = Some((_coreMemory * (vmemFactor + (0.5 * retryMultipler))) + "G")
-    jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
+    jobName = configNamespace + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
   }
 
   override def setupRetry(): Unit = {

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, submodule = 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, submodule = 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/WriteDependencies.scala

@@ -36,7 +36,7 @@ object WriteDependencies extends Logging with Configurable {
     val cache: mutable.Map[String, Int] = mutable.Map()
     for (function <- functions) {
       val baseName = function match {
-        case f: Configurable => f.configName
+        case f: Configurable => f.configNamespace
         case f               => f.getClass.getSimpleName
       }
       cache += baseName -> (cache.getOrElse(baseName, 0) + 1)

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", submodule = "python", freeVar = false)
+  executable = config("exe", default = "python", namespace = "python", freeVar = false)
 
   protected var pythonScriptName: String = _
 

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

@@ -37,7 +37,7 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
   private[summary] var summaryQScripts: List[SummaryQScript] = Nil
 
   /** Name of the pipeline in the summary */
-  var summaryName = configName
+  var summaryName = configNamespace
 
   /** Must return a map with used settings for this pipeline */
   def summarySettings: Map[String, Any]
@@ -103,7 +103,7 @@ trait SummaryQScript extends BiopetQScript { qscript: QScript =>
       if (writeSummary.md5sum) {
         if (!SummaryQScript.md5sumCache.contains(file)) {
           val md5sum = new Md5sum(this) {
-            override def configName = "md5sum"
+            override def configNamespace = "md5sum"
 
             override def cmdLine: String = super.cmdLine + " || " +
               required("echo") + required("error_on_capture  " + input.toString) + " > " + required(output)

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

@@ -75,16 +75,16 @@ class WriteSummary(val root: Configurable) extends InProcessFunction with Config
         def fetchVersion(f: QFunction): Option[(String, Any)] = {
           f match {
             case f: BiopetJavaCommandLineFunction with Version =>
-              Some(f.configName -> Map("version" -> f.getVersion.getOrElse(None),
+              Some(f.configNamespace -> Map("version" -> f.getVersion.getOrElse(None),
                 "java_md5" -> BiopetCommandLineFunction.executableMd5Cache.getOrElse(f.executable, None),
                 "java_version" -> f.getJavaVersion,
                 "jar_path" -> f.jarFile))
             case f: BiopetCommandLineFunction with Version =>
-              Some(f.configName -> Map("version" -> f.getVersion.getOrElse(None),
+              Some(f.configNamespace -> Map("version" -> f.getVersion.getOrElse(None),
                 "md5" -> BiopetCommandLineFunction.executableMd5Cache.getOrElse(f.executable, None),
                 "path" -> f.executable))
             case f: Configurable with Version =>
-              Some(f.configName -> Map("version" -> f.getVersion.getOrElse(None)))
+              Some(f.configNamespace -> Map("version" -> f.getVersion.getOrElse(None)))
             case _ => None
           }
         }