diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
index 001fb9d17b858320d22549bae321ca0b820eac12..b8f4ea4efa3ea8cfed563c2b82651c0001b794f7 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
@@ -9,40 +9,40 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
- override def afterGraph {
- super.afterGraph
-
- min_mapping_quality_score = config("minMappingQualityScore", default = 20)
- if (config.contains("scattercount")) scatterCount = config("scattercount")
- if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
- this.sample_ploidy = config("ploidy")
- nct = config("threads", default = 1)
- bamOutput = config("bamOutput")
- memoryLimit = Option(nct.getOrElse(1) * 2)
- if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
- if (config.contains("output_mode")) {
- import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
- config("output_mode").asString match {
- case "EMIT_ALL_CONFIDENT_SITES" => output_mode = EMIT_ALL_CONFIDENT_SITES
- case "EMIT_ALL_SITES" => output_mode = EMIT_ALL_SITES
- case "EMIT_VARIANTS_ONLY" => output_mode = EMIT_VARIANTS_ONLY
- case e => logger.warn("output mode '" + e + "' does not exist")
- }
+ min_mapping_quality_score = config("minMappingQualityScore", default = 20)
+ scatterCount = config("scattercount", default = 1)
+ if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
+ this.sample_ploidy = config("ploidy")
+ if (config.contains("bamOutput")) bamOutput = config("bamOutput")
+ if (config.contains("allSitePLs")) allSitePLs = config("allSitePLs")
+ if (config.contains("output_mode")) {
+ import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
+ config("output_mode").asString match {
+ case "EMIT_ALL_CONFIDENT_SITES" => output_mode = EMIT_ALL_CONFIDENT_SITES
+ case "EMIT_ALL_SITES" => output_mode = EMIT_ALL_SITES
+ case "EMIT_VARIANTS_ONLY" => output_mode = EMIT_VARIANTS_ONLY
+ case e => logger.warn("output mode '" + e + "' does not exist")
}
+ }
- if (config("inputtype", default = "dna").asString == "rna") {
- dontUseSoftClippedBases = config("dontusesoftclippedbases", default = true)
- stand_call_conf = config("stand_call_conf", default = 5)
- stand_emit_conf = config("stand_emit_conf", default = 0)
- } else {
- dontUseSoftClippedBases = config("dontusesoftclippedbases", default = false)
- stand_call_conf = config("stand_call_conf", default = 5)
- stand_emit_conf = config("stand_emit_conf", default = 0)
- }
+ if (config("inputtype", default = "dna").asString == "rna") {
+ dontUseSoftClippedBases = config("dontusesoftclippedbases", default = true)
+ stand_call_conf = config("stand_call_conf", default = 5)
+ stand_emit_conf = config("stand_emit_conf", default = 0)
+ } else {
+ dontUseSoftClippedBases = config("dontusesoftclippedbases", default = false)
+ stand_call_conf = config("stand_call_conf", default = 5)
+ stand_emit_conf = config("stand_emit_conf", default = 0)
+ }
+
+ override def afterGraph {
+ super.afterGraph
if (bamOutput != null && nct.getOrElse(1) > 1) {
- nct = Option(1)
+ threads = 1
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
}
+ nct = Some(threads)
+ memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))
}
def useGvcf() {
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 10036b6bc88bfb9061a2d6e8e78eb5bc821db4da..8bac4aaf68c33a245da877d460bc26abb9ebe564 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
@@ -50,7 +50,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
def init() {
if (outputName == null && sampleID != null) outputName = sampleID
- else if (outputName == null) outputName = "noname"
+ else if (outputName == null) outputName = config("output_name", default = "noname")
if (outputDir == null) throw new IllegalStateException("Missing Output directory on gatk module")
else if (!outputDir.endsWith("/")) outputDir += "/"
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 97cc2bd46adc5826c560b9a0759f4379e2ff5f0b..4a5b25f7a5b816fe32ad39897a334a6e13fe1eda 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
@@ -15,13 +15,11 @@
*/
package nl.lumc.sasc.biopet.core
-//import java.io.BufferedInputStream
import java.io.File
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.queue.QException
import org.broadinstitute.gatk.queue.function.CommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
-//import scala.io.Source
import scala.sys.process.{ Process, ProcessLogger }
import scala.util.matching.Regex
import java.io.FileInputStream
@@ -53,7 +51,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
override def freezeFieldValues() {
checkExecutable
afterGraph
- jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
+ if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
if (threads == 0) threads = getThreads(defaultThreads)
if (threads > 1) nCoresRequest = Option(threads)
@@ -62,8 +60,8 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
vmem = config("vmem")
if (vmem.isEmpty && defaultVmem.nonEmpty) vmem = Some(defaultVmem)
}
- if (vmem != null) jobResourceRequests :+= "h_vmem=" + vmem
- jobName = configName + ":" + firstOutput.getName
+ if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
+ jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
super.freezeFieldValues()
}