diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
index 928f14329ef0747da3f1d7652c35beb560d9751d..e04af3d5b469330e9f0b72f0f265dd0d50004086 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
@@ -54,29 +54,43 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
}
protected def checkExecutable {
- try if (executable != null) {
- val buffer = new StringBuffer()
- val cmd = Seq("which", executable)
- val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
- if (process.exitValue == 0) {
- executable = buffer.toString
- 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")
+ if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
+ try if (executable != null) {
+ if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
+ val oldExecutable = executable
+ val buffer = new StringBuffer()
+ val cmd = Seq("which", executable)
+ val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
+ if (process.exitValue == 0) {
+ executable = buffer.toString
+ 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")
+ }
+ BiopetCommandLineFunctionTrait.executableCache += oldExecutable -> executable
+ BiopetCommandLineFunctionTrait.executableCache += executable -> executable
+ } else {
+ executable = BiopetCommandLineFunctionTrait.executableCache(executable)
+ }
+
+ if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
+ val is = new FileInputStream(executable)
+ val cnt = is.available
+ val bytes = Array.ofDim[Byte](cnt)
+ is.read(bytes)
+ is.close()
+ val temp = MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
+ BiopetCommandLineFunctionTrait.executableMd5Cache += executable -> temp
+ }
+
+ addJobReportBinding("md5sum_exe", BiopetCommandLineFunctionTrait.executableMd5Cache(executable))
+ } catch {
+ case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
}
-
- val is = new FileInputStream(executable)
- val cnt = is.available
- val bytes = Array.ofDim[Byte](cnt)
- is.read(bytes)
- is.close()
- val md5: String = MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
-
- addJobReportBinding("md5sum_exe", md5)
- } catch {
- case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
+ } else {
+ addJobReportBinding("md5sum_exe", BiopetCommandLineFunctionTrait.executableMd5Cache(executable))
}
}
@@ -138,4 +152,6 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
object BiopetCommandLineFunctionTrait {
import scala.collection.mutable.Map
private val versionCache: Map[String, String] = Map()
+ private val executableMd5Cache: Map[String, String] = Map()
+ private val executableCache: Map[String, String] = Map()
}
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
index 0acc5f348c65a878926d64e3482008ff037505f8..11e094c6c155cd08f8051238b047e7d1bba648af 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
@@ -1,6 +1,8 @@
package nl.lumc.sasc.biopet.core
+import java.io.File
import java.util.Properties
+import nl.lumc.sasc.biopet.core.config.Config
import org.apache.log4j.Logger
object BiopetExecutable extends Logging {
@@ -82,6 +84,11 @@ object BiopetExecutable extends Logging {
return command.get
}
+ // Read config files
+ for (t <- 0 until args.size) {
+ if (args(t) == "-config" || args(t) == "--config_ile") Config.global.loadConfigFile(new File(args(t + 1)))
+ }
+
args match {
case Array("version") => {
println("version: " + getVersion)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index 015c48dd1525dde3e91d49099a7e48f89c709e69..cf4ee286b0a7c40aa128f3d1fc807e8badce9515 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.core
import java.io.File
import java.io.PrintWriter
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.config.{ Config, Configurable }
import org.broadinstitute.gatk.utils.commandline.Argument
import org.broadinstitute.gatk.queue.QSettings
import org.broadinstitute.gatk.queue.function.QFunction
@@ -25,7 +25,6 @@ trait BiopetQScript extends Configurable {
var functions: Seq[QFunction]
final def script() {
- for (file <- configfiles) globalConfig.loadConfigFile(file)
if (!outputDir.endsWith("/")) outputDir += "/"
init
biopetScript
@@ -33,7 +32,7 @@ trait BiopetQScript extends Configurable {
case f: BiopetCommandLineFunctionTrait => f.afterGraph
case _ =>
}
- val configReport = globalConfig.getReport
+ val configReport = Config.global.getReport
val configReportFile = new File(outputDir + qSettings.runName + ".configreport.txt")
configReportFile.getParentFile.mkdir
val writer = new PrintWriter(configReportFile)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
index 9b8197de1acdc1ca492760b931180e09176068bb..32977c6f615aa3cfda69539afee31c330d8e418a 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala
@@ -7,9 +7,13 @@ import org.apache.log4j.WriterAppender
import org.apache.log4j.helpers.DateLayout
trait Logging {
- protected val logger = Logger.getLogger(getClass.getSimpleName.split("\\$").last)
+ def logger = Logging.logger
+}
+
+object Logging {
+ val logger = Logger.getLogger("Logging")
- private[core] val logLayout = new DateLayout() {
+ val logLayout = new DateLayout() {
val ignoresThrowable = false
def format(event: org.apache.log4j.spi.LoggingEvent): String = {
val calendar: Calendar = Calendar.getInstance
@@ -18,10 +22,13 @@ trait Logging {
val formattedDate: String = formatter.format(calendar.getTime)
var logLevel = event.getLevel.toString
while (logLevel.size < 6) logLevel += " "
- logLevel + " [" + formattedDate + "] [" + event.getLoggerName + "] " + event.getMessage + "\n"
+ val className = event.getLocationInformation.getClassName.split("\\.").last.split("\\$").head
+ logLevel + " [" + formattedDate + "] [" + className + "] " + event.getMessage + "\n"
}
}
- private[core] val stderrAppender = new WriterAppender(logLayout, sys.process.stderr)
+
+ val stderrAppender = new WriterAppender(logLayout, sys.process.stderr)
+
logger.setLevel(org.apache.log4j.Level.INFO)
- logger.addAppender(stderrAppender)
-}
+ logger.addAppender(Logging.stderrAppender)
+}
\ No newline at end of file
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index 97bc2e5e6b1d244ec8ee1b0fc3d96ad028421192..81f81f26aafed8ba2126217acec768232077084d 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -1,6 +1,6 @@
package nl.lumc.sasc.biopet.core
-import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.config.{ Config, Configurable }
trait MultiSampleQScript extends BiopetQScript {
type LibraryOutput <: AbstractLibraryOutput
@@ -20,7 +20,7 @@ trait MultiSampleQScript extends BiopetQScript {
final def runSamplesJobs() {
samplesConfig = config("samples")
if (samplesConfig == null) samplesConfig = Map()
- if (globalConfig.contains("samples")) for ((key, value) <- samplesConfig) {
+ if (Config.global.contains("samples")) for ((key, value) <- samplesConfig) {
var sample = Configurable.any2map(value)
if (!sample.contains("ID")) sample += ("ID" -> key)
if (sample("ID") == key) {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
index 0a5dc8428cec541fd6cf1b967893e7266bcb1575..6cbef5b674f11d7bdffd7e5e9f766214932a8ba2 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala
@@ -9,10 +9,10 @@ trait ToolCommand extends MainCommand with Logging {
abstract class AbstractOptParser extends scopt.OptionParser[Args](commandName) {
opt[Unit]("log_nostderr") foreach { _ =>
- logger.removeAppender(stderrAppender)
+ logger.removeAppender(Logging.stderrAppender)
} text ("No output to stderr")
opt[File]("log_file") foreach { x =>
- logger.addAppender(new WriterAppender(logLayout, new java.io.PrintStream(x)))
+ logger.addAppender(new WriterAppender(Logging.logLayout, new java.io.PrintStream(x)))
} text ("Log file") valueName ("<file>")
opt[String]('l', "log_level") foreach { x =>
x.toLowerCase match {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
index c35a1fdd71501b3ecddd721185ee99a271de9434..e373d7b5332651cb45006643a60d61ef1a24a438 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Config.scala
@@ -1,7 +1,7 @@
package nl.lumc.sasc.biopet.core.config
import java.io.File
-import org.broadinstitute.gatk.queue.util.Logging
+import nl.lumc.sasc.biopet.core.Logging
import argonaut._, Argonaut._
import scalaz._, Scalaz._
@@ -104,7 +104,9 @@ class Config(var map: Map[String, Any]) extends Logging {
override def toString(): String = map.toString
}
-object Config {
+object Config extends Logging {
+ val global = new Config
+
def valueToMap(input: Any): Map[String, Any] = {
input match {
case m: Map[_, _] => return m.asInstanceOf[Map[String, Any]]
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
index 62cd27d6bc12f12283a43e065441306c6eecc178..7f6f6cb8e3e958a3ad121411dbe133603f45fdb4 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/config/Configurable.scala
@@ -6,16 +6,16 @@ import scala.language.implicitConversions
trait Configurable extends Logging {
val root: Configurable
- val globalConfig: Config = if (root != null) root.globalConfig else new Config()
+ //val globalConfig: Config = if (root != null) root.globalConfig else new Config()
def configPath: List[String] = if (root != null) root.configFullPath else List()
protected lazy val configName = getClass.getSimpleName.toLowerCase
protected lazy val configFullPath = configName :: configPath
var defaults: scala.collection.mutable.Map[String, Any] = if (root != null) scala.collection.mutable.Map(root.defaults.toArray: _*)
else scala.collection.mutable.Map()
- val config = new ConfigFuntions
+ val config = new ConfigFunctions
- protected class ConfigFuntions {
+ protected class ConfigFunctions {
def apply(key: String, default: Any = null, submodule: String = null, required: Boolean = false, freeVar: Boolean = true): ConfigValue = {
val m = if (submodule != null) submodule else configName
val p = if (submodule != null) configName :: configPath else configPath
@@ -29,15 +29,15 @@ trait Configurable extends Logging {
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 globalConfig(m, p, key, freeVar)
- else return globalConfig(m, p, key, d, freeVar)
+ if (d == null) return Config.global(m, p, key, freeVar)
+ else return Config.global(m, p, key, d, freeVar)
}
def contains(key: String, submodule: String = null, freeVar: Boolean = true) = {
val m = if (submodule != null) submodule else configName
val p = if (submodule != null) configName :: configPath else configPath
- globalConfig.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
+ Config.global.contains(m, p, key, freeVar) || !(Config.getValueFromMap(defaults.toMap, ConfigValueIndex(m, p, key, freeVar)) == None)
}
}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index fdb2493a6b48e05f3bca9d7f79760887016a81b6..f30960a2b0932e59dc6cf3ba3881cf5291fda62d 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -26,7 +26,6 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
var wholeGenome = false
def init() {
- for (file <- configfiles) globalConfig.loadConfigFile(file)
if (outputDir == null) throw new IllegalStateException("Missing Output directory on BamMetrics module")
else if (!outputDir.endsWith("/")) outputDir += "/"
if (config.contains("target_bed")) {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
index b0366e5f5bcf0036ed5e64c8ee5c7f3dcb87c8ef..a120a1374f82b2b748571c15e9b40750730192a9 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
@@ -18,10 +18,10 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
var input_R2: File = _
@Argument(doc = "Skip Trim fastq files", shortName = "skiptrim", required = false)
- var skipTrim: Boolean = false
+ var skipTrim: Boolean = config("skiptrim", default = false)
@Argument(doc = "Skip Clip fastq files", shortName = "skipclip", required = false)
- var skipClip: Boolean = false
+ var skipClip: Boolean = config("skipclip", default = false)
@Argument(doc = "Sample name", shortName = "sample", required = true)
var sampleName: String = _
@@ -43,9 +43,6 @@ class Flexiprep(val root: Configurable) extends QScript with BiopetQScript {
val summary = new FlexiprepSummary(this)
def init() {
- for (file <- configfiles) globalConfig.loadConfigFile(file)
- if (!skipTrim) skipTrim = config("skiptrim", default = false)
- if (!skipClip) skipClip = config("skipclip", default = false)
if (input_R1 == null) throw new IllegalStateException("Missing R1 on flexiprep module")
if (outputDir == null) throw new IllegalStateException("Missing Output directory on flexiprep module")
if (sampleName == null) throw new IllegalStateException("Missing Sample name on flexiprep module")
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
index d26f27e9c07fbc2fb5c6df5117fb89c6f7c8b470..23740daf48fd2f7c4e04e17d7aafe01b24950781 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
@@ -18,18 +18,15 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
@Input(doc = "Gvcf files", shortName = "I", required = false)
var gvcfFiles: List[File] = Nil
- @Argument(doc = "Reference", shortName = "R", required = false)
- var reference: File = _
+ var reference: File = config("reference")
@Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
- var dbsnp: File = _
+ var dbsnp: File = config("dbsnp")
def init() {
if (config.contains("gvcffiles")) for (file <- config("gvcffiles").getList) {
gvcfFiles ::= file.toString
}
- if (reference == null) reference = config("reference")
- if (dbsnp == null) dbsnp = config("dbsnp")
if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
else if (!outputDir.endsWith("/")) outputDir += "/"
}
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
index 37adabdc507c686256fbd732d39e72558e079d0b..5ed4f062982c6b64516d651b50c9008953f4b7a2 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
@@ -13,10 +13,10 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
var inputGvcfs: List[File] = Nil
@Argument(doc = "Reference", shortName = "R", required = false)
- var reference: File = _
+ var reference: File = config("reference")
@Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
- var dbsnp: File = _
+ var dbsnp: File = config("dbsnp")
@Argument(doc = "OutputName", required = false)
var outputName: String = "genotype"
@@ -28,8 +28,6 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
var samples: List[String] = Nil
def init() {
- if (reference == null) reference = config("reference")
- if (dbsnp == null) dbsnp = config("dbsnp")
if (outputFile == null) outputFile = outputDir + outputName + ".vcf.gz"
if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
else if (!outputDir.endsWith("/")) outputDir += "/"
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
index 9af84cbbba2212472450b94aefdbe49bc457fd43..c5bb656d039e5bb2b9b19792d03f7a7d2cfaa75c 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
@@ -27,17 +27,17 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
var mergeGvcfs: Boolean = false
@Argument(doc = "Joint variantcalling", shortName = "jointVariantCalling", required = false)
- var jointVariantcalling = false
+ var jointVariantcalling: Boolean = config("joint_variantcalling", default = false)
@Argument(doc = "Joint genotyping", shortName = "jointGenotyping", required = false)
- var jointGenotyping = false
+ var jointGenotyping: Boolean = config("joint_genotyping", default = false)
- var singleSampleCalling = true
- var reference: File = _
- var dbsnp: File = _
+ var singleSampleCalling = config("single_sample_calling", default = true)
+ var reference: File = config("reference", required = true)
+ var dbsnp: File = config("dbsnp")
var gvcfFiles: List[File] = Nil
var finalBamFiles: List[File] = Nil
- var useAllelesOption: Boolean = _
+ var useAllelesOption: Boolean = config("use_alleles_option", default = false)
class LibraryOutput extends AbstractLibraryOutput {
var mappedBamFile: File = _
@@ -49,15 +49,9 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
}
def init() {
- useAllelesOption = config("use_alleles_option", default = false)
- reference = config("reference", required = true)
- dbsnp = config("dbsnp")
if (config.contains("target_bed")) {
defaults ++= Map("gatk" -> Map(("intervals" -> config("target_bed").getStringList)))
}
- jointVariantcalling = config("joint_variantcalling", default = false)
- jointGenotyping = config("joint_genotyping", default = false)
- singleSampleCalling = config("single_sample_calling", default = true)
if (config.contains("gvcfFiles"))
for (file <- config("gvcfFiles").getList)
gvcfFiles :+= file.toString
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
index e4899798f13141998c9f8f81fe4988c31f4f9660..23e6c81b6bb93156f237e3d0bd8bd198dda753b7 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
@@ -24,10 +24,10 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
var rawVcfInput: File = _
@Argument(doc = "Reference", shortName = "R", required = false)
- var reference: File = _
+ var reference: File = config("reference", required = true)
@Argument(doc = "Dbsnp", shortName = "dbsnp", required = false)
- var dbsnp: File = _
+ var dbsnp: File = config("dbsnp")
@Argument(doc = "OutputName", required = false)
var outputName: String = _
@@ -35,21 +35,14 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
@Argument(doc = "Sample name", required = false)
var sampleID: String = _
- var preProcesBams: Option[Boolean] = None
+ var preProcesBams: Option[Boolean] = config("pre_proces_bams", default = true)
var variantcalling: Boolean = true
- var doublePreProces: Option[Boolean] = None
- var useHaplotypecaller: Option[Boolean] = None
- var useUnifiedGenotyper: Option[Boolean] = None
- var useAllelesOption: Option[Boolean] = None
+ var doublePreProces: Option[Boolean] = config("double_pre_proces", default = true)
+ var useHaplotypecaller: Option[Boolean] = config("use_haplotypecaller", default = true)
+ var useUnifiedGenotyper: Option[Boolean] = config("use_unifiedgenotyper", default = false)
+ var useAllelesOption: Option[Boolean] = config("use_alleles_option", default = false)
def init() {
- if (useAllelesOption == None) useAllelesOption = config("use_alleles_option", default = false)
- if (preProcesBams == None) preProcesBams = config("pre_proces_bams", default = true)
- if (doublePreProces == None) doublePreProces = config("double_pre_proces", default = true)
- if (useHaplotypecaller == None) useHaplotypecaller = config("use_haplotypecaller", default = true)
- if (useUnifiedGenotyper == None) useUnifiedGenotyper = config("use_unifiedgenotyper", default = false)
- if (reference == null) reference = config("reference", required = true)
- if (dbsnp == null) dbsnp = config("dbsnp")
if (outputName == null && sampleID != null) outputName = sampleID
else if (outputName == null) outputName = "noname"
if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
index 067012e443ee81958910e07fa0eb8c8361293bd8..2669dc2b38ce5751f14208e41ca64714f1489759 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVcfSampleCompare.scala
@@ -16,7 +16,7 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
var vcfFiles: List[File] = _
@Argument(doc = "Reference", shortName = "R", required = false)
- var reference: File = _
+ var reference: File = config("reference")
@Argument(doc = "Target bed", shortName = "targetBed", required = false)
var targetBed: List[File] = Nil
@@ -29,7 +29,6 @@ class GatkVcfSampleCompare(val root: Configurable) extends QScript with BiopetQS
def generalSampleDir = outputDir + "samples/"
def init() {
- if (reference == null) reference = config("reference")
if (config.contains("target_bed"))
for (bed <- config("target_bed").getList)
targetBed :+= bed.toString
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index fb159e9b8b05b83e5f08fa0664a6ae9ecdd41b7a..d254b51d7baabafbbb7cc0302f8abb5c25a660b2 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -69,7 +69,7 @@ class Gentrap(val root: Configurable) extends QScript with BiopetQScript {
var cExonBase: Boolean = _
def init() {
- for (file <- configfiles) globalConfig.loadConfigFile(file)
+
}
def biopetScript() {
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index ad1406f566dab1c061e7cb52f7feae8e9c260df9..68194858396b0e34b35ed85cc04d31c369d39e03 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -36,13 +36,13 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var skipMetrics: Boolean = false
@Argument(doc = "Aligner", shortName = "ALN", required = false)
- var aligner: String = _
+ var aligner: String = config("aligner", default = "bwa")
@Argument(doc = "Reference", shortName = "R", required = false)
- var reference: File = _
+ var reference: File = config("reference")
@Argument(doc = "Chunking", shortName = "chunking", required = false)
- var chunking: Boolean = false
+ var chunking: Boolean = config("chunking", false)
@ClassType(classOf[Int])
@Argument(doc = "Number of chunks, when not defined pipeline will automatic calculate number of chunks", shortName = "numberChunks", required = false)
@@ -50,62 +50,48 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
// Readgroup items
@Argument(doc = "Readgroup ID", shortName = "RGID", required = false)
- var RGID: String = _
+ var RGID: String = config("RGID")
@Argument(doc = "Readgroup Library", shortName = "RGLB", required = false)
- var RGLB: String = _
+ var RGLB: String = config("RGLB")
@Argument(doc = "Readgroup Platform", shortName = "RGPL", required = false)
- var RGPL: String = _
+ var RGPL: String = config("RGPL", default = "illumina")
@Argument(doc = "Readgroup platform unit", shortName = "RGPU", required = false)
- var RGPU: String = _
+ var RGPU: String = config("RGPU", default = "na")
@Argument(doc = "Readgroup sample", shortName = "RGSM", required = false)
- var RGSM: String = _
+ var RGSM: String = config("RGSM")
@Argument(doc = "Readgroup sequencing center", shortName = "RGCN", required = false)
- var RGCN: String = _
+ var RGCN: String = config("RGCN")
@Argument(doc = "Readgroup description", shortName = "RGDS", required = false)
- var RGDS: String = _
+ var RGDS: String = config("RGDS")
@Argument(doc = "Readgroup sequencing date", shortName = "RGDT", required = false)
var RGDT: Date = _
@Argument(doc = "Readgroup predicted insert size", shortName = "RGPI", required = false)
- var RGPI: Int = _
+ var RGPI: Int = config("RGPI")
var paired: Boolean = false
- var defaultAligner = "bwa"
val flexiprep = new Flexiprep(this)
def init() {
- for (file <- configfiles) globalConfig.loadConfigFile(file)
- if (aligner == null) aligner = config("aligner", default = defaultAligner)
- if (reference == null) reference = config("reference")
if (outputDir == null) throw new IllegalStateException("Missing Output directory on mapping module")
else if (!outputDir.endsWith("/")) outputDir += "/"
if (input_R1 == null) throw new IllegalStateException("Missing FastQ R1 on mapping module")
paired = (input_R2 != null)
- if (RGLB == null && config.contains("RGLB")) RGLB = config("RGLB")
- else if (RGLB == null) throw new IllegalStateException("Missing Readgroup library on mapping module")
- if (RGSM == null && config.contains("RGSM")) RGSM = config("RGSM")
- else if (RGLB == null) throw new IllegalStateException("Missing Readgroup sample on mapping module")
- if (RGID == null && config.contains("RGID")) RGID = config("RGID")
- else if (RGID == null && RGSM != null && RGLB != null) RGID = RGSM + "-" + RGLB
+ if (RGLB == null) throw new IllegalStateException("Missing Readgroup library on mapping module")
+ if (RGLB == null) throw new IllegalStateException("Missing Readgroup sample on mapping module")
+ if (RGID == null && RGSM != null && RGLB != null) RGID = RGSM + "-" + RGLB
else if (RGID == null) throw new IllegalStateException("Missing Readgroup ID on mapping module")
- if (RGPL == null) RGPL = config("RGPL", "illumina")
- if (RGPU == null) RGPU = config("RGPU", "na")
- if (RGCN == null && config.contains("RGCN")) RGCN = config("RGCN")
- if (RGDS == null && config.contains("RGDS")) RGDS = config("RGDS")
-
if (outputName == null) outputName = RGID
- if (!chunking && numberChunks.isDefined) chunking = true
- if (!chunking) chunking = config("chunking", false)
if (chunking) {
if (numberChunks.isEmpty) {
if (config.contains("numberchunks")) numberChunks = config("numberchunks", default = None)
@@ -311,10 +297,6 @@ object Mapping extends PipelineCommand {
val mapping = new Mapping(root)
logger.debug("Mapping runconfig: " + runConfig)
- var inputType = ""
- if (runConfig.contains("inputtype")) inputType = runConfig("inputtype").toString
- else inputType = root.config("inputtype", "dna").getString
- if (inputType == "rna") mapping.defaultAligner = "star-2pass"
if (runConfig.contains("R1")) mapping.input_R1 = new File(runConfig("R1").toString)
if (runConfig.contains("R2")) mapping.input_R2 = new File(runConfig("R2").toString)
mapping.paired = (mapping.input_R2 != null)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
index 937b84261a20935025aeb79c4f555a7fdfb6827b..7a826e9bb6412d053ff240b1c7e5bc08e9258388 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
@@ -20,15 +20,15 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
def this() = this(null)
@Input(doc = "countBed", required = false)
- var countBed: File = _
+ var countBed: File = config("count_bed")
@Input(doc = "squishedCountBed, by suppling this file the auto squish job will be skipped", required = false)
- var squishedCountBed: File = _
+ var squishedCountBed: File = config("squished_count_bed")
@Input(doc = "Transcriptome, used for generation of tag library", required = false)
- var transcriptome: File = _
+ var transcriptome: File = config("transcriptome")
- var tagsLibrary: File = _
+ var tagsLibrary: File = config("tags_library")
defaults ++= Map("bowtie" -> Map(
"m" -> 1,
@@ -50,10 +50,6 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
def init() {
if (!outputDir.endsWith("/")) outputDir += "/"
- if (countBed == null) countBed = config("count_bed")
- if (squishedCountBed == null) squishedCountBed = config("squished_count_bed")
- if (tagsLibrary == null) tagsLibrary = config("tags_library")
- if (transcriptome == null) transcriptome = config("transcriptome")
if (transcriptome == null && tagsLibrary == null)
throw new IllegalStateException("No transcriptome or taglib found")
if (countBed == null && squishedCountBed == null)
@@ -140,7 +136,7 @@ class Sage(val root: Configurable) extends QScript with MultiSampleQScript {
val mapping = new Mapping(this)
mapping.skipFlexiprep = true
mapping.skipMarkduplicates = true
- mapping.defaultAligner = "bowtie"
+ mapping.aligner = config("aligner", default = "bowtie")
mapping.input_R1 = prefixFastq.output
mapping.RGLB = runConfig("ID").toString
mapping.RGSM = sampleConfig("ID").toString
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
index 10aef464b610c43571398d6285d3ddd7bc9c5b3c..a428eb693211f1787c72990a7f68ef8df225cc95 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
@@ -21,7 +21,7 @@ import org.broadinstitute.gatk.queue.engine.JobRunInfo
class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
def this() = this(null)
- var reference: File = _
+ var reference: File = config("reference", required = true)
var finalBamFiles: List[File] = Nil
class LibraryOutput extends AbstractLibraryOutput {
@@ -34,8 +34,6 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
}
override def init() {
- for (file <- configfiles) globalConfig.loadConfigFile(file)
- reference = config("reference", required = true)
if (outputDir == null)
throw new IllegalStateException("Output directory is not specified in the config / argument")
else if (!outputDir.endsWith("/"))
@@ -124,7 +122,7 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
if (runConfig.contains("R1")) {
val mapping = new Mapping(this)
- mapping.defaultAligner = "stampy"
+ mapping.aligner = config("aligner", default = "stampy")
mapping.skipFlexiprep = false
mapping.skipMarkduplicates = true // we do the dedup marking using Sambamba
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
index 9c364cf62da705beaa94cb682b59a33c7e3329ef..3d11e5452d63b6c87a472ec22ee05454a66d7496 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
@@ -74,16 +74,16 @@ object MpileupToVcf extends ToolCommand {
opt[String]('s', "sample") required () action { (x, c) =>
c.copy(sample = x)
}
- opt[Int]("minDP") required () action { (x, c) =>
+ opt[Int]("minDP") action { (x, c) =>
c.copy(minDP = x)
}
- opt[Int]("minAP") required () action { (x, c) =>
+ opt[Int]("minAP") action { (x, c) =>
c.copy(minAP = x)
}
- opt[Double]("homoFraction") required () action { (x, c) =>
+ opt[Double]("homoFraction") action { (x, c) =>
c.copy(homoFraction = x)
}
- opt[Int]("ploidy") required () action { (x, c) =>
+ opt[Int]("ploidy") action { (x, c) =>
c.copy(ploidy = x)
}
}