diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index 6b99ca1706a0280a88b881e74e11a644e5ef1ab2..750cbee21adea6c059d939aad518ca9aed0eb06e 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/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")
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 ab6692982d698ef8d4ea41593f07b55b01671db8..d9085369f0316b6a0474fe02cd15ef07c683713a 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
@@ -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)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
index 5a574b729fb7fa4c7b27c674845f069fd01cb4ca..fc2f95e4e33f54dca689568bb48cb8489ed3e65d 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+++ b/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")
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
index ada8007283b76122005cc5d4e6a0a39c161ea1aa..0479bbb754d62a13e4e7d99bf6ac949b8cd69aec 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+++ b/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")
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
index 5ddaa72341c6a35b6cc9070c6d50cc48e80b7551..fed464a7391ad3f618e3755c2b8addc3cfb608b1 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
+++ b/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
diff --git a/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala b/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
index 7a5a541899981f9a3a6bf25396ea23d64afd60d3..8dceeb52502cf5b150bc3fa4e41ccdb9cb6aebae 100644
--- a/public/biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
+++ b/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"
}
}
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
index 1d536084f976312300c091744a99a01a4ae4c3e3..4c69bf57c8be5332aeb3f1cc3d1f78b2ae204007 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/config/Config.scala
+++ b/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
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 476c4c4435290a9229bc926695cb9153d996d75a..1613109b2fc34fae7336b21d8382116b28a297e1 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
@@ -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
}
}
}
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 8853a1183870f304c3529c43c569365c33437a27..37e851cf1572848a648bcb45ff5b7a51edeb0a68 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
@@ -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"
)
)
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index ecf5bb0d8ff66d7ce9d595f8786919c9db11601a..2be78c7226036ef90021d8bfc144a225c0460ab5 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/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
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
index 6c444bed885b3b4219728bf38423156b3d545064..8de84c5081db4b9801222c6853e2b185a54741e6 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+++ b/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 {
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 aeab29b7d697093726674b263f916faf77bccd7d..baf8d34dc40f017a0907775e5b2a3c32b70c8915 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
@@ -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()
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 f7f9dc2ab2d916e22c0a6858663f1a43773f7f22..cce952717b29e94556d3535cab4c5830d33a1cfe 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
@@ -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)
}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index d033594c6e42663427108baf12038b7eed6fb3f6..724470df1091228bbdaf928b49ae7024f2bb70bd 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/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)
+ override def defaults = 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
+ )
+ )
/** Adds output merge jobs for the given expression mode */
// TODO: can we combine the enum with the file extension (to reduce duplication and potential errors)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 0d93e48ecd82b7c8d4fdae8b336c6aae06c785c4..aeff9d559027f53cb1ab2715b0119f2f32451421 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -97,13 +97,12 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** location of summary file */
def summaryFile = new File(outputDir, sampleId.getOrElse("x") + "-" + libId.getOrElse("x") + ".summary.json")
- override def defaults = ConfigUtils.mergeMaps(
- Map(
- "gsnap" -> Map(
- "batch" -> 4,
- "format" -> "sam"
- )
- ), super.defaults)
+ override def defaults = Map("gsnap" -> Map("batch" -> 4))
+
+ override def fixedValues = Map(
+ "gsnap" -> Map("format" -> "sam"),
+ "bowtie" -> Map("sam" -> true)
+ )
/** File to add to the summary */
def summaryFiles: Map[String, File] = Map("output_bamfile" -> finalBamFile, "input_R1" -> input_R1,
diff --git a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index 2ee8c3b1930aff553234f6f3860d7c13e0818783..c8b81c0c4d31d6424db74390390c758096478838 100644
--- a/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -36,21 +36,22 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
var transcriptome: Option[File] = config("transcriptome")
var tagsLibrary: Option[File] = config("tags_library")
- override def defaults = ConfigUtils.mergeMaps(Map("bowtie" -> Map(
- "m" -> 1,
- "k" -> 1,
- "best" -> true,
- "strata" -> true,
- "seedmms" -> 1
- ), "mapping" -> Map(
- "aligner" -> "bowtie",
- "skip_flexiprep" -> true,
- "skip_markduplicates" -> true
- ), "flexiprep" -> Map(
- "skip_clip" -> true,
- "skip_trim" -> true
- ), "strandSensitive" -> true
- ), super.defaults)
+ override def defaults = Map(
+ "bowtie" -> Map(
+ "m" -> 1,
+ "k" -> 1,
+ "best" -> true,
+ "strata" -> true,
+ "seedmms" -> 1
+ ), "mapping" -> Map(
+ "aligner" -> "bowtie",
+ "skip_flexiprep" -> true,
+ "skip_markduplicates" -> true
+ ), "flexiprep" -> Map(
+ "skip_clip" -> true,
+ "skip_trim" -> true
+ ), "strandSensitive" -> true
+ )
def summaryFile: File = new File(outputDir, "Sage.summary.json")
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 f9cbddd1d75560c3c5e5c538a1ac0080dacd620a..26302af07fb2abac8007faaf9dbc55e16fca23e1 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
@@ -199,11 +199,11 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
val vcfFilter = new VcfFilter(qscript) {
override def configName = "vcffilter"
- 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 = new File(outputDir, bamFile.getName.stripSuffix(".bam") + ".raw.filter.vcf.gz")
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 7c3cc327858be60bb3d299e550c0f4244b656560..6ee0776713a5391296719ac6edc83819777fcf31 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
@@ -38,9 +38,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
inputFiles :+= new InputFile(inputVCF)
}
- override def defaults = ConfigUtils.mergeMaps(Map(
+ override def defaults = Map(
"varianteffectpredictor" -> Map("everything" -> true)
- ), super.defaults)
+ )
//defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true))