Commit eb605a1f authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge branch 'fix-268' into 'develop'

Fix 268

Fixes #268 

See merge request !318
parents acbbc173 e16d2e05
...@@ -23,9 +23,7 @@ import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension ...@@ -23,9 +23,7 @@ import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.utils.Logging import nl.lumc.sasc.biopet.utils.Logging
import org.broadinstitute.gatk.queue.{ QScript, QSettings } import org.broadinstitute.gatk.queue.{ QScript, QSettings }
import org.broadinstitute.gatk.queue.function.QFunction import org.broadinstitute.gatk.queue.function.QFunction
import org.broadinstitute.gatk.queue.function.scattergather.ScatterGatherableFunction
import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging } import org.broadinstitute.gatk.queue.util.{ Logging => GatkLogging }
import org.broadinstitute.gatk.utils.commandline.Argument
/** Base for biopet pipeline */ /** Base for biopet pipeline */
trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript => trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
...@@ -99,7 +97,8 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript => ...@@ -99,7 +97,8 @@ trait BiopetQScript extends Configurable with GatkLogging { qscript: QScript =>
inputFiles.foreach { i => inputFiles.foreach { i =>
if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}") if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
else if (!i.file.canRead) Logging.addError(s"Input file can not be read: ${i.file}") if (!i.file.canRead) Logging.addError(s"Input file can not be read: ${i.file}")
if (!i.file.isAbsolute) Logging.addError(s"Input file should be an absulute path: ${i.file}")
} }
functions.filter(_.jobOutputFile == null).foreach(f => { functions.filter(_.jobOutputFile == null).foreach(f => {
......
...@@ -39,7 +39,7 @@ class VarscanMpileup2cns(val root: Configurable) extends Varscan { ...@@ -39,7 +39,7 @@ class VarscanMpileup2cns(val root: Configurable) extends Varscan {
var vcfSampleList: Option[File] = config("vcf_sample_list") var vcfSampleList: Option[File] = config("vcf_sample_list")
var variants: Option[Int] = config("variants") var variants: Option[Int] = config("variants")
override def defaultCoreMemory = 6.0 override def defaultCoreMemory = 8.0
override def beforeGraph(): Unit = { override def beforeGraph(): Unit = {
val validValues: Set[Int] = Set(0, 1) val validValues: Set[Int] = Set(0, 1)
......
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