diff --git a/docs/developer/example-pipeline.md b/docs/developer/example-pipeline.md
index f4f6bb9d76da32118d6a89c3026165bd1669211e..432c4ec5711e09ab20539c0527f0efa2175bd125 100644
--- a/docs/developer/example-pipeline.md
+++ b/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
{
diff --git a/docs/general/memory.md b/docs/general/memory.md
index 95e38862e440238f0502fae40f1371cbc38459c8..c0fc6033c656550454fe11a27541c338d261ca9e 100644
--- a/docs/general/memory.md
+++ b/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
diff --git a/docs/pipelines/basty.md b/docs/pipelines/basty.md
index fdb21ae3ca1ed6cdcb1f373aa3265433b30f03e6..7da41338f2fc7f8327ca558eec9ca6d00948ad57 100644
--- a/docs/pipelines/basty.md
+++ b/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 |
diff --git a/docs/pipelines/shiva.md b/docs/pipelines/shiva.md
index ead5f91acca3309831b4c00c56a3e17e3127d431..3c2bbaa98978f352ea5cd4ac5fe4a0b75286eb6c 100644
--- a/docs/pipelines/shiva.md
+++ b/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 |
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
index 11560ea25e216a49515b618f03bbb9604accc731..e4fdf3d2d26875e7795802fbda50c00ac118c875 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
+++ b/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
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
index 86e51353983b35d5248fa7958b1f5c3c8ebffac0..244fae67a31938f4eadaa5228c979bf4a4cd9011 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
+++ b/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"
}
}
diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
index f1b326b7017b129eaf6edf0d44014af4f9507b7b..8be9ae9a79066c233c1c92b6dfb2f9cb1432385f 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
+++ b/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"
diff --git a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala b/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
index 14207e5a829de7fd7cae4738a10fd9f6b28c5546..f4576e5a10d380e572891cae1160d665ebbe8746 100644
--- a/protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
+++ b/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"
diff --git a/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala b/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
index 1482e2afeb2633f6ed3000c2f399dfc5a0f1bad6..4a75d99e00d3a21324c8d5459d891e6435691185 100644
--- a/public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+++ b/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"
diff --git a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala b/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
index 675d4d7557be2edf84c41494edfaa30af9d13a78..3202d4f37db17d1bb9b824c89e948e44d82fb829 100644
--- a/public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
+++ b/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
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
index a413c8bad83199c38a1b156a67118d2e7262b50c..4a41248e5653ee9dd6a1e32e64845447b4198b06 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/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
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
index 5722871028d92aeddd2723c22971a2e08e51107a..be3d05fcfa0dfb0a8a39d200cfa4c64f6802bfd9 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
+++ b/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)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
index af98f00969a0c0b0b77c59db903f7b3346ce3274..936096971632109dea09bfac739ae5e3f8c1e5e1 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetPipe.scala
+++ b/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))
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 54a23127c6037e115e5586c70a6b206eb277cd13..9545911b9a4de84f11a6fe0742ca2877aed7ae20 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/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 */
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
index 8ef7eb746cd744021656c56ae28f3226c800a0a7..ac01cfa15a963e851cad1cc81ff627d030d39a9a 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/CommandLineResources.scala
+++ b/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 = {
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index 86804903c16a0cbda64bf338a902fa6ac2dc5bb1..840a67d0abec0ba4dbb8b784d8a99ee1190dfb20 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/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)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
index 108ee694e54fc4dd126dfc82f90adb7470602cde..a43cb3890bcf3521e3be6645b4e175c59f84d143 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
+++ b/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)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
index e4c0b269568dbabbea6231edece9d76b5dc38dc2..40d8cd32108fc5babfb95bf5cb4b81b526f34f47 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/extensions/PythonCommandLineFunction.scala
+++ b/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 = _
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
index 0e947ba6c7d3bbf144c98feb1b7cb21601c6629f..619a31dacbdeeea9272198efc3f343ba109ccdcb 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/SummaryQScript.scala
+++ b/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)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
index b888438d7ba2150fdb156067fbdc39bfe5db9b7f..56cab45bc8555b6cf88a40ac145054cd526e5c2e 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/summary/WriteSummary.scala
+++ b/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
}
}
diff --git a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
index 5d4f89f8de4a1fcdebc69ab5ad81ad2f0881ce50..e4c31c51aa07581ba0bd6a3781af205e5b15238c 100644
--- a/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
+++ b/public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala
@@ -310,7 +310,7 @@ object WriteSummaryTest {
stats: Map[String, Any] = Map(),
c: Map[String, Any] = Map()) = new BiopetJavaCommandLineFunction with Summarizable with Version {
override def globalConfig = new Config(c)
- override def configName = "java_command"
+ override def configNamespace = "java_command"
def root: Configurable = null
def summaryStats: Map[String, Any] = stats
def summaryFiles: Map[String, File] = files
@@ -335,7 +335,7 @@ object WriteSummaryTest {
c: Map[String, Any] = Map()) =
new CommandLineFunction with Configurable with Summarizable with Version {
override def globalConfig = new Config(c)
- override def configName = "version_command"
+ override def configNamespace = "version_command"
def root: Configurable = null
def summaryFiles: Map[String, File] = files
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index ee375163166ca858393bb95ee9f3bc7850896f84..6242da5d7378caf98add3d3c2888245621762895 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/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", submodule = "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)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
index 2017d4c30da42cce13d4b10ac7ca3142e3f5f178..bc8ae1e7a3072db7afeaa346425c38bb83a8e633 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+++ b/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", submodule = "perl", default = "perl")
+ executable = config("exe", namespace = "perl", default = "perl")
var vepScript: String = config("vep_script")
@Input(doc = "input VCF", required = true)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
index 2291df063b26293132bbd95c9f8ccf56c8ddfd13..56a76ebbf8e443a4524433bf66b0271d3f4e5c6a 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/Bcftools.scala
+++ b/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", submodule = "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)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
index 1933cbea798a11c314f267df611aa09bccb5f92c..02c1ed90a5e5007f9232e0a0523ae4b362c8dae2 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/Bedtools.scala
+++ b/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", submodule = "bedtools")
+ executable = config("exe", default = "bedtools", namespace = "bedtools")
def versionCommand = executable + " --version"
def versionRegex = """bedtools (.*)""".r
}
\ No newline at end of file
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
index 56f3060b1eb917019d9f6cfe40f353778c3fb7c4..f7d4b3313582c72893a02aae7ebbfa1b833d903d 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
+++ b/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", submodule = "java", freeVar = false)
+ var executable: String = config("java", default = "java", namespace = "java", freeVar = false)
override def subPath = "gatk" :: super.subPath
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
index a509f2e7b77149501091170b36087ed067971797..21f3019e19f56711aa1a35cdc3ac556a62a6baf8 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala
+++ b/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", submodule = "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)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
index 5f8365efc793ca1903ee6eba609d6b87f3ebbf65..68e7e205a5213b058b18ecf85b73936ff8506b64 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/macs2/Macs2.scala
+++ b/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", submodule = "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)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala
index b7a3c161a2e3992751923c06332205845e0403ff..09c518f617fe75023663ff4871e1caae678d4c6e 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/manwe/Manwe.scala
+++ b/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", submodule = "manwe")
+ executable = config("exe", default = "manwe", namespace = "manwe")
var manweConfig: File = createManweConfig(None)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
index b12ff9584da1090aa90970dbbd137c0bb6b792e9..f5153a987b7cbb78e59022bb601c0d816b1e3675 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
+++ b/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", submodule = "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)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
index f0703990369edb6791ffb11b61bdbbf0927a270a..ca8133896411ea979117dfcc0251e41625f45d36 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/Samtools.scala
+++ b/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", submodule = "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)
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
index f0da112c99bea4bb016d13ce8b5b04edc691f430..01f5f37c34f02cddefa335dbdb1257ac1f16b3bf 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+++ b/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 +
- " module: " + value.requestIndex.module,
+ " namespace: " + value.requestIndex.module,
if (value.requestIndex.path != Nil) " path: " + value.requestIndex.path.mkString("->") else null)
exist
}
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
index bc0f207df80f003d7120d466a3eea7c0ffcc040c..786d1a1b02db257f7d28a74ab384f83c416ae63c 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Configurable.scala
@@ -30,10 +30,10 @@ trait Configurable extends ImplicitConversions {
def configPath: List[String] = if (root != null) root.configFullPath else Nil
/** Gets name of module for config */
- def configName = getClass.getSimpleName.toLowerCase
+ def configNamespace = getClass.getSimpleName.toLowerCase
/** ull path with module in there */
- def configFullPath: List[String] = configPath ::: configName :: Nil
+ def configFullPath: List[String] = configPath ::: configNamespace :: Nil
/** Map to store defaults for config */
def defaults: Map[String, Any] = Map()
@@ -69,7 +69,7 @@ trait Configurable extends ImplicitConversions {
def getConfigPath(sample: String = null, library: String = null, submodule: String = null) = {
(if (sample != null) "samples" :: sample :: Nil else Nil) :::
(if (library != null) "libraries" :: library :: Nil else Nil) :::
- (if (submodule != null) configPath ::: configName :: Nil else configPath)
+ (if (submodule != null) configPath ::: configNamespace :: Nil else configPath)
}
/** Class is used for retrieval of config values */
@@ -92,7 +92,7 @@ trait Configurable extends ImplicitConversions {
*
* @param key Name of value
* @param default Default value if not found
- * @param submodule 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,
- submodule: 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 (submodule != null) submodule else configName
- val p = if (path == null) getConfigPath(s, l, submodule) ::: 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 submodule 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,
- submodule: 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 (submodule != null) submodule else configName
- val p = if (path == null) getConfigPath(s, l, submodule) ::: 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
}
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
index aad5042bd7ad944e5daa2ce2ecb79006807b7bcc..0901d6c8022c74c0b5adcb9f0c43f6e1529cc29e 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/Rscript.scala
+++ b/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", submodule = "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)
diff --git a/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala b/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
index 37e851cf1572848a648bcb45ff5b7a51edeb0a68..a252e65366bc60952e0244d8574b4008ce6d3f1a 100644
--- a/public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/config/ConfigurableTest.scala
+++ b/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)
}
}
@@ -52,7 +52,7 @@ class ConfigurableTest extends TestNGSuite with Matchers {
@Test def testConfigurable(): Unit = {
val classC = new ClassC {
- override def configName = "classc"
+ override def configNamespace = "classc"
override val globalConfig = new Config(ConfigurableTest.map)
override val fixedValues = Map("fixed" -> "fixed")
}
diff --git a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
index da5d79939fd3729fb8838ab26bbe1a2d2d2bfb00..77345a0858f4ae2a5926b497c8df89114ffb64a5 100644
--- a/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+++ b/public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
@@ -37,7 +37,7 @@ import org.testng.annotations.{ AfterClass, DataProvider, Test }
class CarpTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Carp = {
new Carp() {
- override def configName = "carp"
+ override def configNamespace = "carp"
override def globalConfig = new Config(map)
qSettings = new QSettings
qSettings.runName = "test"
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index ab87244ee6329c0163d91660df6e8f57f866949a..c1a04ed85efe48a27fff3fe14cb789e98d3504a7 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -204,7 +204,7 @@ class Flexiprep(val root: Configurable) extends QScript with SummaryQScript with
fqSync.outputStats = new File(outDir, s"${sampleId.getOrElse("x")}-${libId.getOrElse("x")}.sync.stats")
val pipe = new BiopetFifoPipe(this, fqSync :: Nil) {
- override def configName = "qc-cmd"
+ override def configNamespace = "qc-cmd"
override def beforeGraph(): Unit = {
fqSync.beforeGraph()
diff --git a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
index 1f00c07a01e073d29e63c21e246d1c3c2dbc69d0..2af324fad3d2815be4c51d191e4b849692c81945 100644
--- a/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+++ b/public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
@@ -36,7 +36,7 @@ class FlexiprepTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Flexiprep = {
new Flexiprep() {
- override def configName = "flexiprep"
+ override def configNamespace = "flexiprep"
override def globalConfig = new Config(map)
qSettings = new QSettings
qSettings.runName = "test"
diff --git a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
index 49e2eb4ec48baca659afe4559a9943507bf16aab..ae1f8d7400da3ecd24934cc73fef362f0c278cf4 100644
--- a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
+++ b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleTest.scala
@@ -39,7 +39,7 @@ import org.testng.annotations._
class GearsSingleTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): GearsSingle = {
new GearsSingle {
- override def configName = "gearssingle"
+ override def configNamespace = "gearssingle"
override def globalConfig = new Config(map)
diff --git a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
index dddd88458379feb532e02dd4b7990b5a63e4d201..cda46755da89d7af2679a77f4e23edb142567fcb 100644
--- a/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
+++ b/public/gears/src/test/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTest.scala
@@ -32,7 +32,7 @@ import org.testng.annotations.{ DataProvider, Test, AfterClass }
class GearsTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Gears = {
new Gears {
- override def configName = "gears"
+ override def configNamespace = "gears"
override def globalConfig = new Config(map)
diff --git a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
index 81e97ab6a22aa7ea93e7dec4769219540ef60dff..73a25ef561cb2363f7b4e930b8e0fb5187a8827a 100644
--- a/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
+++ b/public/gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
@@ -31,7 +31,7 @@ abstract class GentrapTestAbstract(val expressionMeasure: String) extends TestNG
def initPipeline(map: Map[String, Any]): Gentrap = {
new Gentrap() {
- override def configName = "gentrap"
+ override def configNamespace = "gentrap"
override def globalConfig = new Config(map)
// disable dict file check since it is based on the reference file name (which we can't modify here since
// we use the mock /usr/bin/test file
diff --git a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
index cce528aaa5f10f796dd06c34f45860b689ccd12e..7b8f289df558dfa2667fd44cbdcfc0b3874926b6 100644
--- a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+++ b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
@@ -35,7 +35,7 @@ import org.testng.annotations.{ BeforeClass, AfterClass, DataProvider, Test }
abstract class AbstractTestMapping(val aligner: String) extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Mapping = {
new Mapping {
- override def configName = "mapping"
+ override def configNamespace = "mapping"
override def globalConfig = new Config(map)
qSettings = new QSettings
qSettings.runName = "test"
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index f0fe2c1291d647815f8d336902fbd944f6312f3f..76aee99b4f3b1c857edc4f402aaae1133f313a55 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -36,15 +36,15 @@ trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegio
Some(shiva)
}
- /** Method to make the variantcalling submodule 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"
- override def configName: String = "shivavariantcalling"
+ override def configNamespace: String = "shivavariantcalling"
override def configPath: List[String] = super.configPath ::: "multisample" :: Nil
}
else new ShivaVariantcalling(qscript) {
- override def configName = "shivavariantcalling"
+ override def configNamespace = "shivavariantcalling"
}
}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
index f08b4cc18402e995375f14f1095e922883b8dc98..06f876979fb3ae541be76758d031174cb6c93e8b 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+++ b/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, submodule = caller.configName)
- val decompose: Boolean = config("execute_vt_decompose", default = false, submodule = caller.configName)
+ 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
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
index 8c1613526e56e5f1d4d77ce6cd336ab2fee4578a..d978be672b518ff3246162cab3f5b8d0371be33e 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/RawVcf.scala
@@ -33,7 +33,7 @@ class RawVcf(val root: Configurable) extends Variantcaller {
val rawFiles = inputBams.map {
case (sample, bamFile) =>
val mp = new SamtoolsMpileup(this) {
- override def configName = "samtoolsmpileup"
+ override def configNamespace = "samtoolsmpileup"
override def defaults = Map("samtoolsmpileup" -> Map("disable_baq" -> true, "min_map_quality" -> 1))
}
mp.input :+= bamFile
@@ -44,7 +44,7 @@ class RawVcf(val root: Configurable) extends Variantcaller {
add(mp | m2v)
val vcfFilter = new VcfFilter(this) {
- override def configName = "vcffilter"
+ override def configNamespace = "vcffilter"
override def defaults = Map("min_sample_depth" -> 8,
"min_alternate_depth" -> 2,
"min_samples_pass" -> 1,
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
index 7e3f1ccdfa0b7d2f4b842f247476c9f5028c5a23..b0eaaa4303b9725ce88c2856d3d050060196140f 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
@@ -40,7 +40,7 @@ import scala.collection.mutable.ListBuffer
class ShivaSvCallingTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): ShivaSvCalling = {
new ShivaSvCalling {
- override def configName = "shivasvcalling"
+ override def configNamespace = "shivasvcalling"
override def globalConfig = new Config(ConfigUtils.mergeMaps(map, ShivaSvCallingTest.config))
qSettings = new QSettings
qSettings.runName = "test"
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
index 31777668d11df48a3ad99a663d60aad6e7666966..c2249f15511d241428ef6f7d8f39b4bbc41e1143 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
@@ -36,7 +36,7 @@ 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"
diff --git a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index b1699c7b97132b1df20c88d49c6202164fa89227..d86e46c7e9ef21dfcdd5a67f779e46adc2b23483 100644
--- a/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
@@ -40,7 +40,7 @@ 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"
diff --git a/public/tinycap/src/test/scala/nl/lucm/sasc/biopet/pipelines/tinycap/TinyCapTest.scala b/public/tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
similarity index 98%
rename from public/tinycap/src/test/scala/nl/lucm/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
rename to public/tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
index b8ec5c3ab159b584c5935bc87e29892799216a71..7275b4349ec04a0e39cc45693173201bff1cc17f 100644
--- a/public/tinycap/src/test/scala/nl/lucm/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
+++ b/public/tinycap/src/test/scala/nl/lumc/sasc/biopet/pipelines/tinycap/TinyCapTest.scala
@@ -35,7 +35,7 @@ class TinyCapTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): TinyCap = {
new TinyCap() {
- override def configName = "tinycap"
+ override def configNamespace = "tinycap"
override def globalConfig = new Config(map)
diff --git a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala b/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
index 1ccb0ea95fedc96d6e967e073ef80a6c3abc0195..2e3ffe26a1735dbea0f664bf8c4c957bd7262f7b 100644
--- a/public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+++ b/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, submodule = "manwe")
- val isPublic: Boolean = config("varda_is_public", default = true, submodule = "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 *"), submodule = "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)