Commit 044fe79f authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Library fix for Queue/GATK 3.2

parent 398500a6
......@@ -5,7 +5,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
class CalculateHsMetrics(val root:Configurable) extends Picard {
javaMainClass = "net.sf.picard.analysis.directed.CalculateHsMetrics"
javaMainClass = "picard.analysis.directed.CalculateHsMetrics"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: File = _
......
......@@ -5,7 +5,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
class CollectGcBiasMetrics(val root:Configurable) extends Picard {
javaMainClass = "net.sf.picard.analysis.CollectGcBiasMetrics"
javaMainClass = "picard.analysis.CollectGcBiasMetrics"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: Seq[File] = Nil
......
......@@ -5,7 +5,7 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
class CollectInsertSizeMetrics(val root:Configurable) extends Picard {
javaMainClass = "net.sf.picard.analysis.CollectInsertSizeMetrics"
javaMainClass = "picard.analysis.CollectInsertSizeMetrics"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: File = _
......
......@@ -5,8 +5,8 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output, Argument}
class MarkDuplicates(val root:Configurable) extends Picard {
javaMainClass = "net.sf.picard.sam.MarkDuplicates"
javaMainClass = "picard.sam.MarkDuplicates"
@Input(doc="The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: List[File] = Nil
......
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