diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
index 147398ac798c077da0722b2078f7ea21c666b7d1..3d1b5585028f69c01934f0ddfc0d54c6a9c25169 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
@@ -13,13 +13,13 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
override def subPath = "gatk" :: super.subPath
- jarFile = config("gatk_jar", required = true)
+ jarFile = config("gatk_jar")
override val defaultVmem = "7G"
if (config.contains("intervals")) intervals = config("intervals").asFileList
if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
- reference_sequence = config("reference", required = true)
+ reference_sequence = config("reference")
if (config.contains("gatk_key")) gatk_key = config("gatk_key")
if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
}
diff --git a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index c76139133f23cf434884ad69ccc9dafc69b2cac9..be4566211351a3d077877d1a99cf8be6ba0f58cd 100644
--- a/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -35,7 +35,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
var jointGenotyping: Boolean = config("joint_genotyping", default = false)
var singleSampleCalling = config("single_sample_calling", default = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
var useAllelesOption: Boolean = config("use_alleles_option", default = false)
val externalGvcfs = config("external_gvcfs_files", default = Nil).asFileList
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 8bac4aaf68c33a245da877d460bc26abb9ebe564..47715e26adb11f0ed73520d2769ca55120a58d93 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
@@ -30,7 +30,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
var rawVcfInput: File = _
@Argument(doc = "Reference", shortName = "R", required = false)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Argument(doc = "OutputName", required = false)
var outputName: String = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 4a5b25f7a5b816fe32ad39897a334a6e13fe1eda..83aa87155236e9b2752407fb4bd39ce21dc36824 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -66,7 +66,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
super.freezeFieldValues()
}
- protected def checkExecutable {
+ protected[core] def checkExecutable {
if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
try if (executable != null) {
if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
@@ -79,8 +79,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
val file = new File(executable)
executable = file.getCanonicalPath
} else {
- logger.error("executable: '" + executable + "' not found, please check config")
- throw new QException("executable: '" + executable + "' not found, please check config")
+ BiopetQScript.addError("executable: '" + executable + "' not found, please check config")
}
BiopetCommandLineFunctionTrait.executableCache += oldExecutable -> executable
BiopetCommandLineFunctionTrait.executableCache += executable -> executable
@@ -101,9 +100,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
}
}
- val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache(executable)
- if (md5 == null) addJobReportBinding("md5sum_exe", md5)
- else addJobReportBinding("md5sum_exe", "None")
+ val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache.get(executable)
+ addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
}
final protected def preCmdInternal {
@@ -120,6 +118,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
protected val versionExitcode = List(0) // Can select multiple
private def getVersionInternal: String = {
if (versionCommand == null || versionRegex == null) return "N/A"
+ val exe = new File(versionCommand.trim.split(" ")(0))
+ if (!exe.exists()) return "N/A"
val stdout = new StringBuffer()
val stderr = new StringBuffer()
def outputLog = "Version command: \n" + versionCommand +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 1a3f565880dc3a2bd5450efd86cfa188e647eef4..062d725bafb7050258aaf07e0a0a0444e02aafdc 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -24,14 +24,16 @@ import org.broadinstitute.gatk.queue.function.QFunction
import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
+import scala.collection.mutable.ListBuffer
+
trait BiopetQScript extends Configurable with GatkLogging {
@Argument(doc = "JSON config file(s)", fullName = "config_file", shortName = "config", required = false)
val configfiles: List[File] = Nil
var outputDir: String = {
- val temp = Config.getValueFromMap(Config.global.map, ConfigValueIndex(this.configName, configPath, "output_dir"))
- if (temp.isEmpty) throw new IllegalArgumentException("No output_dir defined in config")
+ val temp = Config.getValueFromMap(globalConfig.map, ConfigValueIndex(this.configName, configPath, "output_dir"))
+ if (temp.isEmpty) ""
else {
val t = temp.get.value.toString
if (!t.endsWith("/")) t + "/" else t
@@ -51,8 +53,9 @@ trait BiopetQScript extends Configurable with GatkLogging {
var functions: Seq[QFunction]
final def script() {
- outputDir = config("output_dir", required = true)
- if (!outputDir.endsWith("/")) outputDir += "/"
+ outputDir = config("output_dir")
+ if (outputDir.isEmpty) outputDir = new File(".").getAbsolutePath()
+ else if (!outputDir.endsWith("/")) outputDir += "/"
init
biopetScript
@@ -61,11 +64,17 @@ trait BiopetQScript extends Configurable with GatkLogging {
case _ =>
}
for (function <- functions) function match {
- case f: BiopetCommandLineFunctionTrait => f.afterGraph
- case _ =>
+ case f: BiopetCommandLineFunctionTrait => {
+ f.checkExecutable
+ f.afterGraph
+ }
+ case _ =>
}
- Config.global.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
+ if (new File(outputDir).canWrite) globalConfig.writeReport(qSettings.runName, outputDir + ".log/" + qSettings.runName)
+ else BiopetQScript.addError("Output dir: '" + outputDir + "' is not writeable")
+
+ BiopetQScript.checkErrors
}
def add(functions: QFunction*) // Gets implemeted at org.broadinstitute.sting.queue.QScript
@@ -73,5 +82,29 @@ trait BiopetQScript extends Configurable with GatkLogging {
function.isIntermediate = isIntermediate
add(function)
}
-
}
+
+object BiopetQScript extends Logging {
+ private val errors: ListBuffer[Exception] = ListBuffer()
+
+ def addError(error: String, debug: String = null): Unit = {
+ val msg = error + (if (debug != null && logger.isDebugEnabled) "; " + debug else "")
+ errors.append(new Exception(msg))
+ }
+
+ protected def checkErrors: Unit = {
+ if (!errors.isEmpty) {
+ logger.error("*************************")
+ logger.error("Biopet found some errors:")
+ if (logger.isDebugEnabled) {
+ for (e <- errors) {
+ logger.error(e.getMessage)
+ logger.debug(e.getStackTrace.mkString("Stack trace:\n", "\n", "\n"))
+ }
+ } else {
+ errors.map(_.getMessage).sorted.distinct.foreach(logger.error(_))
+ }
+ throw new IllegalStateException("Biopet found errors")
+ }
+ }
+}
\ No newline at end of file
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index eb76502c8593a9e970ea2c95b9152569dfffb389..4184f29afacc7f6afcf6dc9d0eb45f9eddfc1993 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -28,7 +28,7 @@ trait MultiSampleQScript extends BiopetQScript {
@Argument(doc = "Only Sample", shortName = "sample", required = false)
private val onlySamples: List[String] = Nil
- require(Config.global.map.contains("samples"), "No Samples found in config")
+ require(globalConfig.map.contains("samples"), "No Samples found in config")
/**
* Sample class with basic functions build in
@@ -80,7 +80,7 @@ trait MultiSampleQScript extends BiopetQScript {
/** returns a set with library names */
protected def libIds: Set[String] = {
- ConfigUtils.getMapFromPath(Config.global.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
+ ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
}
/** Adds sample jobs */
@@ -125,7 +125,7 @@ trait MultiSampleQScript extends BiopetQScript {
val samples: Map[String, Sample] = sampleIds.map(id => id -> makeSample(id)).toMap
/** Returns a list of all sampleIDs */
- protected def sampleIds: Set[String] = ConfigUtils.any2map(Config.global.map("samples")).keySet
+ protected def sampleIds: Set[String] = ConfigUtils.any2map(globalConfig.map("samples")).keySet
/** Runs addAndTrackJobs method for each sample */
final def addSamplesJobs() {
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
index 4ea65cb5a7fc7ceb1226853d47687a0865c818d0..e25e8ef508188adbd5f767b20ca1f688c4eed922 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
@@ -133,11 +133,11 @@ class Config(var map: Map[String, Any]) extends Logging {
*/
protected[config] def apply(module: String, path: List[String], key: String, default: Any = null, freeVar: Boolean = true): ConfigValue = {
val requestedIndex = ConfigValueIndex(module, path, key, freeVar)
- if (contains(requestedIndex)) return foundCache(requestedIndex)
+ if (contains(requestedIndex)) foundCache(requestedIndex)
else if (default != null) {
defaultCache += (requestedIndex -> ConfigValue(requestedIndex, null, default, freeVar))
- return defaultCache(requestedIndex)
- } else throw new IllegalStateException("Value in config could not be found but it seems required, index: " + requestedIndex)
+ defaultCache(requestedIndex)
+ } else ConfigValue(requestedIndex, null, null, freeVar)
}
def writeReport(id: String, directory: String): Unit = {
@@ -174,7 +174,7 @@ class Config(var map: Map[String, Any]) extends Logging {
val fullEffective = ConfigUtils.mergeMaps(effectiveFound, effectiveDefaultFound)
val fullEffectiveWithNotFound = ConfigUtils.mergeMaps(fullEffective, notFound)
- writeMapToJsonFile(Config.global.map, "input")
+ writeMapToJsonFile(this.map, "input")
writeMapToJsonFile(found, "found")
writeMapToJsonFile(effectiveFound, "effective.found")
writeMapToJsonFile(effectiveDefaultFound, "effective.defaults")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
index 54e6dfd170a8cb2e68f5c63dd8ca2675513cee7d..51997ccb8a12fb5c3a234e5e7d95c001dd704b4f 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.utils.ConfigUtils.ImplicitConversions
trait Configurable extends ImplicitConversions {
/** Should be object of parant object */
val root: Configurable
+ val globalConfig: Config = if (root != null) root.globalConfig else Config.global
/** subfix to the path */
def subPath: List[String] = Nil
@@ -79,7 +80,6 @@ trait Configurable extends ImplicitConversions {
* @param key Name of value
* @param default Default value if not found
* @param submodule Adds to the path
- * @param required Default false, if true and value is not found this function will raise an exception
* @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"
@@ -88,7 +88,6 @@ trait Configurable extends ImplicitConversions {
def apply(key: String,
default: Any = null,
submodule: String = null,
- required: Boolean = false,
freeVar: Boolean = true,
sample: String = null,
library: String = null): ConfigValue = {
@@ -100,14 +99,8 @@ trait Configurable extends ImplicitConversions {
val value = Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar))
if (value.isDefined) value.get.value else default
}
- if (!contains(key, submodule, freeVar, sample = s, library = l) && d == null) {
- if (required) {
- Logging.logger.error("Value in config could not be found but it is required, key: " + key + " module: " + m + " path: " + p)
- throw new IllegalStateException("Value in config could not be found but it is required, key: " + key + " module: " + m + " path: " + p)
- } else return null
- }
- if (d == null) return Config.global(m, p, key, freeVar = freeVar)
- else return Config.global(m, p, key, d, freeVar)
+ if (d == null) globalConfig(m, p, key, freeVar = freeVar)
+ else globalConfig(m, p, key, d, freeVar)
}
/**
@@ -129,7 +122,7 @@ trait Configurable extends ImplicitConversions {
val m = if (submodule != null) submodule else configName
val p = path(s, l, submodule)
- Config.global.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
+ globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
}
}
}
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
index e7467ced6086d1f6cc88d46dc110dc77bafc3809..a2ca78b4c52e0a0faa5a4a67ebd7998096a68cf9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/workaround/BiopetQCommandLine.scala
@@ -81,19 +81,15 @@ object BiopetQCommandLine extends GatkLogging {
Runtime.getRuntime.addShutdownHook(shutdownHook)
+ CommandLineProgram.start(qCommandLine, argv)
try {
- CommandLineProgram.start(qCommandLine, argv)
- try {
- Runtime.getRuntime.removeShutdownHook(shutdownHook)
- qCommandLine.shutdown()
- } catch {
- case e: Exception => /* ignore, example 'java.lang.IllegalStateException: Shutdown in progress' */
- }
- if (CommandLineProgram.result != 0)
- System.exit(CommandLineProgram.result)
+ Runtime.getRuntime.removeShutdownHook(shutdownHook)
+ qCommandLine.shutdown()
} catch {
- case e: Exception => CommandLineProgram.exitSystemWithError(e)
+ case e: Exception => /* ignore, example 'java.lang.IllegalStateException: Shutdown in progress' */
}
+ if (CommandLineProgram.result != 0)
+ System.exit(CommandLineProgram.result)
}
}
@@ -114,21 +110,28 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
private var qScriptClasses: File = _
private var shuttingDown = false
+ /**
+ * we modified this in Biopet to skip compiling and show full stacktrace again
+ */
private lazy val qScriptPluginManager = {
qScriptClasses = IOUtils.tempDir("Q-Classes-", "", settings.qSettings.tempDirectory)
- //qScriptManager.loadScripts(scripts, qScriptClasses)
- //var temp: Seq[URL] = Seq()
for (t <- scripts) {
val is = getClass.getResourceAsStream(t.getAbsolutePath)
val os = new FileOutputStream(qScriptClasses.getAbsolutePath + "/" + t.getName)
org.apache.commons.io.IOUtils.copy(is, os)
os.close()
- //temp :+= this.getClass.getResource(t.toString)
- //logger.info(this.getClass.getResource(t.toString))
val s = if (t.getName.endsWith("/")) t.getName.substring(0, t.getName.length - 1) else t.getName
pipelineName = s.substring(0, s.lastIndexOf(".")) + "." + System.currentTimeMillis
}
- new PluginManager[QScript](qPluginType, List(qScriptClasses.toURI.toURL))
+
+ // override createByType to pass the correct exceptions
+ new PluginManager[QScript](qPluginType, List(qScriptClasses.toURI.toURL)) {
+ override def createByType(plugintype: Class[_ <: QScript]) = {
+ val noArgsConstructor = plugintype.getDeclaredConstructor()
+ noArgsConstructor.setAccessible(true)
+ noArgsConstructor.newInstance()
+ }
+ }
}
private lazy val qCommandPlugin = {
@@ -186,12 +189,7 @@ class BiopetQCommandLine extends CommandLineProgram with Logging {
//if (settings.run)
script.pullInputs()
script.qSettings = settings.qSettings
- try {
- script.script()
- } catch {
- case e: Exception =>
- throw new UserException.CannotExecuteQScript(script.getClass.getSimpleName + ".script() threw the following exception: " + e, e)
- }
+ script.script()
if (remoteFileConverter != null) {
if (remoteFileConverter.convertToRemoteEnabled)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
index e192a845be6db96d2a754d2d2ff6a5e393d136ca..9ac74448e880d7be01063a3f12bdd613141b34a4 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Bowtie.scala
@@ -29,7 +29,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "R")
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
index fed5e514be34618f41d2e8348eba6d15e67fab29..7bda8792544eea2d863ab06192b51b55ae900077 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
@@ -51,7 +51,7 @@ class Fastqc(val root: Configurable) extends BiopetCommandLineFunction {
override def afterGraph {
this.checkExecutable
- val fastqcDir = executable.substring(0, executable.lastIndexOf("/"))
+ val fastqcDir = new File(executable).getParent
contaminants = contaminants match {
// user-defined contaminants file take precedence
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
index a7bfeab78447e62eee1634c73ca09c880679327e..1db8f6d67c8d892e6188aa750efb40b814fbbf1e 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Stampy.scala
@@ -29,13 +29,13 @@ class Stampy(val root: Configurable) extends BiopetCommandLineFunction {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "ref")
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Input(doc = "The genome prefix.")
- var genome: File = config("genome", required = true)
+ var genome: File = config("genome")
@Input(doc = "The hash prefix")
- var hash: File = config("hash", required = true)
+ var hash: File = config("hash")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
index e0b8bd68bda46a6b3dc6915a54482b093cfd43d6..98ee6de521d499710e186bb2c196d9d471c6aa5d 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/TopHat.scala
@@ -29,7 +29,7 @@ class TopHat(val root: Configurable) extends BiopetCommandLineFunction {
var R2: File = _
@Input(doc = "Bowtie index", shortName = "bti")
- var bowtie_index: File = config("bowtie_index", required = true)
+ var bowtie_index: File = config("bowtie_index")
@Argument(doc = "Output Directory")
var outputDir: String = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
index bfd0a5846e6531b47f285453a2d848b1b7f1bafe..3298702fcfd5cd98e1eaf0bae8f6b059d353d2c9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.scala
@@ -13,7 +13,7 @@ class BwaAln(val root: Configurable) extends Bwa {
var fastq: File = _
@Input(doc = "The reference file for the bam files.", required = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", required = false)
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
index fc790b183b5bae2922a1b5f89ec66fcf4f5b85b2..74cdad0cea290e5a8cdcc2b360fa3fa32444791c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaMem.scala
@@ -29,7 +29,7 @@ class BwaMem(val root: Configurable) extends Bwa {
var R2: File = _
@Input(doc = "The reference file for the bam files.", shortName = "R")
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", shortName = "output")
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
index b857eea014ac52acb9608debb94db9cd75cef929..255811561e732b229b1417c95d866fad4694c0c9 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala
@@ -26,7 +26,7 @@ class BwaSampe(val root: Configurable) extends Bwa {
var saiR2: File = _
@Input(doc = "The reference file for the bam files.", required = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", required = false)
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
index 51f9a0f30eaf73a897fefaa2b6cf69d4e3386b62..8bbf918474e21d2e2837ce01d5bc4490e13bd087 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSamse.scala
@@ -16,7 +16,7 @@ class BwaSamse(val root: Configurable) extends Bwa {
var sai: File = _
@Input(doc = "The reference file for the bam files.", required = true)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Output(doc = "Output file SAM", required = false)
var output: File = _
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
index 7ffcb50d8fec02138c07e4fc95d7608e8bfba72e..9cab9bfc90298f243f6cfdc8e051e7d451a4cf90 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
@@ -35,7 +35,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard {
var outputSummary: File = _
@Argument(doc = "Reference file", required = false)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
@Argument(doc = "Window size", required = false)
var windowSize: Option[Int] = config("windowsize")
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
index 9f1cddb7913cf7846daa72c7b9e695988b3a14c6..2c9165036824f135f9552b69fa3b4085be25fc93 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
@@ -16,6 +16,7 @@
package nl.lumc.sasc.biopet.utils
import java.io.File
+import nl.lumc.sasc.biopet.core.BiopetQScript
import nl.lumc.sasc.biopet.core.Logging
import nl.lumc.sasc.biopet.core.config.ConfigValue
import argonaut._, Argonaut._
@@ -330,14 +331,27 @@ object ConfigUtils extends Logging {
trait ImplicitConversions {
import scala.language.implicitConversions
+ private def requiredValue(value: ConfigValue): Boolean = {
+ val exist = valueExists(value)
+ if (!exist)
+ BiopetQScript.addError("Value does not exist but is required, key: " + value.requestIndex.key +
+ " module: " + value.requestIndex.module,
+ (if (value.requestIndex.path != Nil) " path: " + value.requestIndex.path.mkString("->") else null))
+ exist
+ }
+
+ private def valueExists(value: ConfigValue): Boolean = {
+ value != null && value.value != null && value.value != None
+ }
+
/**
* Convert ConfigValue to File
* @param value Input ConfigValue
* @return
*/
implicit def configValue2file(value: ConfigValue): File = {
- if (value != null && value.value != null && value.value != None) new File(any2string(value.value))
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) new File(any2string(value.value))
+ else new File("")
}
/**
@@ -346,7 +360,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionFile(value: ConfigValue): Option[File] = {
- if (value != null && value.value != null && value.value != None) Some(new File(any2string(value.value)))
+ if (valueExists(value)) Some(new File(any2string(value.value)))
else None
}
@@ -356,8 +370,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2string(value: ConfigValue): String = {
- if (value != null && value.value != null && value.value != None) any2string(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2string(value.value)
+ else ""
}
/**
@@ -366,7 +380,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionString(value: ConfigValue): Option[String] = {
- if (value != null && value.value != null && value.value != None) Some(any2string(value.value))
+ if (valueExists(value)) Some(any2string(value.value))
else None
}
@@ -376,8 +390,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2long(value: ConfigValue): Long = {
- if (value != null && value.value != null && value.value != None) any2long(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2long(value.value)
+ else 0L
}
/**
@@ -386,7 +400,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionLong(value: ConfigValue): Option[Long] = {
- if (value != null && value.value != null && value.value != None) Option(any2long(value.value))
+ if (valueExists(value)) Option(any2long(value.value))
else None
}
@@ -396,8 +410,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2int(value: ConfigValue): Int = {
- if (value != null && value.value != null && value.value != None) any2int(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2int(value.value)
+ else 0
}
/**
@@ -406,7 +420,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionInt(value: ConfigValue): Option[Int] = {
- if (value != null && value.value != null && value.value != None) Option(any2int(value.value))
+ if (valueExists(value)) Option(any2int(value.value))
else None
}
@@ -416,8 +430,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2double(value: ConfigValue): Double = {
- if (value != null && value.value != null && value.value != None) any2double(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2double(value.value)
+ else 0.0
}
/**
@@ -426,7 +440,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionDouble(value: ConfigValue): Option[Double] = {
- if (value != null && value.value != null && value.value != None) Option(any2double(value.value))
+ if (valueExists(value)) Option(any2double(value.value))
else None
}
@@ -436,8 +450,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2float(value: ConfigValue): Float = {
- if (value != null && value.value != null && value.value != None) any2float(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2float(value.value)
+ else 0f
}
/**
@@ -446,7 +460,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionFloat(value: ConfigValue): Option[Float] = {
- if (value != null && value.value != null && value.value != None) Option(any2float(value.value))
+ if (valueExists(value)) Option(any2float(value.value))
else None
}
@@ -456,8 +470,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2boolean(value: ConfigValue): Boolean = {
- if (value != null && value.value != null && value.value != None) any2boolean(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2boolean(value.value)
+ else false
}
/**
@@ -466,7 +480,7 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2optionBoolean(value: ConfigValue): Option[Boolean] = {
- if (value != null && value.value != null && value.value != None) Option(any2boolean(value.value))
+ if (valueExists(value)) Option(any2boolean(value.value))
else None
}
@@ -476,8 +490,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2list(value: ConfigValue): List[Any] = {
- if (value != null && value.value != null && value.value != None) any2list(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2list(value.value)
+ else Nil
}
/**
@@ -486,8 +500,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2stringList(value: ConfigValue): List[String] = {
- if (value != null && value.value != null && value.value != None) any2stringList(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2stringList(value.value)
+ else Nil
}
/**
@@ -496,8 +510,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2stringSet(value: ConfigValue): Set[String] = {
- if (value != null && value.value != null && value.value != None) any2stringList(value.value).toSet
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2stringList(value.value).toSet
+ else Set()
}
/**
@@ -506,8 +520,8 @@ object ConfigUtils extends Logging {
* @return
*/
implicit def configValue2map(value: ConfigValue): Map[String, Any] = {
- if (value != null && value.value != null && value.value != None) any2map(value.value)
- else throw new IllegalStateException("Value does not exist")
+ if (requiredValue(value)) any2map(value.value)
+ else Map()
}
}
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
index 92d0b9f63f60ad1a6c9489ba1d71fd3f25ab6828..b7353b2ad1d4a91cd05340edbd7a61a51e64e266 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
@@ -30,9 +30,6 @@ class ConfigTest extends TestNGSuite with Matchers with ConfigUtils.ImplicitConv
@Test def testApply: Unit = {
ConfigTest.config("m1", Nil, "k1").asString shouldBe "v2"
ConfigTest.config("m1", Nil, "notexist", default = "default").asString shouldBe "default"
- intercept[IllegalStateException] {
- ConfigTest.config("m1", Nil, "notexist")
- }
}
@Test def testMergeConfigs: Unit = {
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
index 1b493f2e14df822b75534fed3722f88917882fe1..19940fde2ecb2c923cdbed79b9fcb85bd1ab4e39 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
@@ -11,10 +11,10 @@ import org.testng.annotations.Test
*/
class ConfigurableTest extends TestNGSuite with Matchers {
@Test def testConfigurable: Unit = {
- Config.global.map = Map()
- Config.global.loadConfigFile(ConfigurableTest.file)
-
- val classC = new ClassC
+ val classC = new ClassC {
+ override def configName = "classc"
+ override val globalConfig = new Config(ConfigurableTest.map)
+ }
classC.configPath shouldBe Nil
classC.configFullPath shouldBe List("classc")
@@ -27,10 +27,6 @@ class ConfigurableTest extends TestNGSuite with Matchers {
classC.classB.get("k1").asString shouldBe "c1"
classC.classB.classA.get("k1").asString shouldBe "c1"
- classC.get("notexist") shouldBe null
- intercept[IllegalStateException] {
- classC.get("notexist", required = true)
- }
classC.get("notexist", default = "default").asString shouldBe "default"
classC.get("k1", freeVar = false).asString shouldBe "c1"
@@ -47,23 +43,24 @@ abstract class Cfg extends Configurable {
def get(key: String,
default: String = null,
submodule: String = null,
- required: Boolean = false,
freeVar: Boolean = true,
sample: String = null,
library: String = null) = {
- config(key, default, submodule, required, freeVar = freeVar, sample = sample, library = library)
+ config(key, default, submodule, freeVar = freeVar, sample = sample, library = library)
}
}
class ClassA(val root: Configurable) extends Cfg
class ClassB(val root: Configurable) extends Cfg {
- val classA = new ClassA(this)
+ lazy val classA = new ClassA(this)
+ // Why this needs to be lazy?
}
class ClassC(val root: Configurable) extends Cfg {
def this() = this(null)
- val classB = new ClassB(this)
+ lazy val classB = new ClassB(this)
+ // Why this needs to be lazy?
}
object ConfigurableTest {
@@ -85,6 +82,4 @@ object ConfigurableTest {
)
)
)
-
- val file = ConfigUtilsTest.writeTemp(ConfigUtils.mapToJson(map).spaces2)
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
index 26f989c5369c4e138ded82620d1d03f0c076ce7c..ddcf887d819eb0edc09bfc5b6a42954115e62192 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
@@ -4,6 +4,7 @@ import java.io.{ PrintWriter, File }
import argonaut.Argonaut._
import argonaut.Json
+import nl.lumc.sasc.biopet.core.BiopetQScript
import nl.lumc.sasc.biopet.core.config.{ ConfigValueIndex, ConfigValue }
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
@@ -170,79 +171,23 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
val index = ConfigValueIndex("test", Nil, "test")
new ImplicitConversions {
configValue2list(ConfigValue(index, index, List(""))) shouldBe List("")
- intercept[IllegalStateException] {
- configValue2list(ConfigValue(index, index, null))
- }
-
configValue2stringList(ConfigValue(index, index, List(""))) shouldBe List("")
- intercept[IllegalStateException] {
- configValue2stringList(ConfigValue(index, index, null))
- }
-
configValue2stringSet(ConfigValue(index, index, List(""))) shouldBe Set("")
- intercept[IllegalStateException] {
- configValue2stringSet(ConfigValue(index, index, null))
- }
var int: Int = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- int = ConfigValue(index, index, null)
- }
-
var long: Long = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- long = ConfigValue(index, index, null)
- }
-
var double: Double = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- double = ConfigValue(index, index, null)
- }
-
var float: Float = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- float = ConfigValue(index, index, null)
- }
-
var boolean: Boolean = ConfigValue(index, index, true)
- intercept[IllegalStateException] {
- boolean = ConfigValue(index, index, null)
- }
-
var intOption: Option[Int] = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- int = ConfigValue(index, index, null)
- }
-
var longOption: Option[Long] = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- long = ConfigValue(index, index, null)
- }
-
var doubleOption: Option[Double] = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- double = ConfigValue(index, index, null)
- }
-
var floatOption: Option[Float] = ConfigValue(index, index, 1)
- intercept[IllegalStateException] {
- float = ConfigValue(index, index, null)
- }
-
var booleanOption: Option[Boolean] = ConfigValue(index, index, true)
- intercept[IllegalStateException] {
- boolean = ConfigValue(index, index, null)
- }
-
var string: String = ConfigValue(index, index, "test")
- intercept[IllegalStateException] {
- string = ConfigValue(index, index, null)
- }
-
var file: File = ConfigValue(index, index, "test")
- intercept[IllegalStateException] {
- file = ConfigValue(index, index, null)
- }
+
+ //TODO: test BiopetQScript error message
}
}
}
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 50ee00b2c5625226a00e0985bbe761ded375237c..21cb069d658623ab5a7b8986e454db6000f927fa 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
@@ -52,10 +52,7 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
* @throws FileNotFoundException if the FastQC data file can not be found.
* @throws IllegalStateException if the module lines have no content or mapping is empty.
*/
- @throws(classOf[FileNotFoundException])
- @throws(classOf[IllegalStateException])
def qcModules: Map[String, FastQCModule] = {
-
val fqModules = Source.fromFile(dataFile)
// drop all the characters before the first module delimiter (i.e. '>>')
.dropWhile(_ != '>')
@@ -93,14 +90,16 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
* @throws NoSuchElementException when the "Basic Statistics" key does not exist in the mapping or
* when a line starting with "Encoding" does not exist.
*/
- @throws(classOf[NoSuchElementException])
- def encoding: String =
- qcModules("Basic Statistics")
- .lines
- .dropWhile(!_.startsWith("Encoding"))
- .head
- .stripPrefix("Encoding\t")
- .stripSuffix("\t")
+ def encoding: String = {
+ if (dataFile.exists) // On a dry run this file does not yet exist
+ qcModules("Basic Statistics") //FIXME: not save
+ .lines
+ .dropWhile(!_.startsWith("Encoding"))
+ .head
+ .stripPrefix("Encoding\t")
+ .stripSuffix("\t")
+ else ""
+ }
/** Case class representing a known adapter sequence */
protected case class AdapterSequence(name: String, seq: String)
@@ -111,32 +110,33 @@ class Fastqc(root: Configurable) extends nl.lumc.sasc.biopet.extensions.Fastqc(r
* @return a [[Set]] of [[AdapterSequence]] objects.
*/
def foundAdapters: Set[AdapterSequence] = {
+ if (dataFile.exists) { // On a dry run this file does not yet exist
+ /** Returns a list of adapter and/or contaminant sequences known to FastQC */
+ def getFastqcSeqs(file: Option[File]): Set[AdapterSequence] = file match {
+ case None => Set.empty[AdapterSequence]
+ case Some(f) =>
+ (for {
+ line <- Source.fromFile(f).getLines()
+ if !line.startsWith("#")
+ values = line.split("\t+")
+ if values.size >= 2
+ } yield AdapterSequence(values(0), values(1))).toSet
+ }
+
+ val found = qcModules.get("Overrepresented sequences") match {
+ case None => Seq.empty[String]
+ case Some(qcModule) =>
+ for (
+ line <- qcModule.lines if !(line.startsWith("#") || line.startsWith(">"));
+ values = line.split("\t") if values.size >= 4
+ ) yield values(3)
+ }
- /** Returns a list of adapter and/or contaminant sequences known to FastQC */
- def getFastqcSeqs(file: Option[File]): Set[AdapterSequence] = file match {
- case None => Set.empty[AdapterSequence]
- case Some(f) =>
- (for {
- line <- Source.fromFile(f).getLines()
- if !line.startsWith("#")
- values = line.split("\t+")
- if values.size >= 2
- } yield AdapterSequence(values(0), values(1))).toSet
- }
-
- val found = qcModules.get("Overrepresented sequences") match {
- case None => Seq.empty[String]
- case Some(qcModule) =>
- for (
- line <- qcModule.lines if !(line.startsWith("#") || line.startsWith(">"));
- values = line.split("\t") if values.size >= 4
- ) yield values(3)
- }
-
- // select full sequences from known adapters and contaminants
- // based on overrepresented sequences results
- (getFastqcSeqs(adapters) ++ getFastqcSeqs(contaminants))
- .filter(x => found.exists(_.startsWith(x.name)))
+ // select full sequences from known adapters and contaminants
+ // based on overrepresented sequences results
+ (getFastqcSeqs(adapters) ++ getFastqcSeqs(contaminants))
+ .filter(x => found.exists(_.startsWith(x.name)))
+ } else Set()
}
/** Summary of the FastQC run, stored in a [[Json]] object */
diff --git a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
index 0fdeee289de9672d917264e3e9dc2d556f6bc48b..05236e13cacae24e5b5dffb408e1aa01b1c297e4 100644
--- a/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
+++ b/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
@@ -27,11 +27,12 @@ class SeqtkSeq(root: Configurable) extends nl.lumc.sasc.biopet.extensions.seqtk.
if (fastqc != null && Q == None) {
val encoding = fastqc.encoding
Q = encoding match {
- case null => None
+ case null => None
case s if (s.contains("Sanger / Illumina 1.9")) => None
- case s if (s.contains("Illumina <1.3")) => Option(64)
- case s if (s.contains("Illumina 1.3")) => Option(64)
- case s if (s.contains("Illumina 1.5")) => Option(64)
+ case s if (s.contains("Illumina <1.3")) => Option(64)
+ case s if (s.contains("Illumina 1.3")) => Option(64)
+ case s if (s.contains("Illumina 1.5")) => Option(64)
+ case _ => None
}
if (Q != None) V = true
}
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 ed55ca382d13346b3cbb7bb4862941ef4da591f5..77dba4b1469eba2d75bedafc9f53be7c23acb557 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
@@ -60,7 +60,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
class Sample(sampleId: String) extends AbstractSample(sampleId) {
def makeLibrary(id: String) = new Library(id)
class Library(libId: String) extends AbstractLibrary(libId) {
- val inputFastq: File = config("R1", required = true)
+ val inputFastq: File = config("R1")
val prefixFastq: File = createFile(".prefix.fastq")
val flexiprep = new Flexiprep(qscript)
diff --git a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index 206c92a69453105fb2034d6cd72cce00f5ab75cd..6e7257c7d94967eac350fc212e7c7b37ebf5dc58 100644
--- a/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -35,7 +35,7 @@ import org.broadinstitute.gatk.queue.engine.JobRunInfo
class Yamsvp(val root: Configurable) extends QScript with BiopetQScript { //with MultiSampleQScript {
def this() = this(null)
- var reference: File = config("reference", required = true)
+ var reference: File = config("reference")
var finalBamFiles: List[File] = Nil
/*
class LibraryOutput extends AbstractLibraryOutput {