Commit 768d77cc authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added sub path instead of submodule

parent 6da08ccb
......@@ -11,13 +11,15 @@ import org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction {
memoryLimit = Option(3)
if (config.contains("gatk_jar")) jarFile = config("gatk_jar")
override def subPath = "gatk" :: super.subPath
jarFile = config("gatk_jar", required = true)
override val defaultVmem = "7G"
if (config.contains("intervals", submodule = "gatk")) intervals = config("intervals", submodule = "gatk").asFileList
if (config.contains("exclude_intervals", submodule = "gatk")) excludeIntervals = config("exclude_intervals", submodule = "gatk").asFileList
reference_sequence = config("reference", submodule = "gatk")
gatk_key = config("gatk_key", submodule = "gatk")
if (config.contains("pedigree", submodule = "gatk")) pedigree = config("pedigree", submodule = "gatk").asFileList
if (config.contains("intervals")) intervals = config("intervals").asFileList
if (config.contains("exclude_intervals")) excludeIntervals = config("exclude_intervals").asFileList
reference_sequence = config("reference")
gatk_key = config("gatk_key")
if (config.contains("pedigree")) pedigree = config("pedigree").asFileList
}
......@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.extensions.bedtools
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
abstract class Bedtools extends BiopetCommandLineFunction {
override def subPath = "bedtools" :: super.subPath
executable = config("exe", default = "bedtools", submodule = "bedtools")
override def versionCommand = executable + " --version"
override val versionRegex = """bedtools (.*)""".r
......
......@@ -18,27 +18,29 @@ package nl.lumc.sasc.biopet.extensions.picard
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import org.broadinstitute.gatk.utils.commandline.{ Argument }
trait Picard extends BiopetJavaCommandLineFunction {
abstract class Picard extends BiopetJavaCommandLineFunction {
override def subPath = "picard" :: super.subPath
@Argument(doc = "VERBOSITY", required = false)
var verbosity: String = config("verbosity", submodule = "picard")
var verbosity: String = config("verbosity")
@Argument(doc = "QUIET", required = false)
var quiet: Boolean = config("quiet", default = false, submodule = "picard")
var quiet: Boolean = config("quiet", default = false)
@Argument(doc = "VALIDATION_STRINGENCY", required = false)
var stringency: String = config("validationstringency", submodule = "picard")
var stringency: String = config("validationstringency")
@Argument(doc = "COMPRESSION_LEVEL", required = false)
var compression: Option[Int] = config("compressionlevel", submodule = "picard")
var compression: Option[Int] = config("compressionlevel")
@Argument(doc = "MAX_RECORDS_IN_RAM", required = false)
var maxRecordsInRam: Option[Int] = config("maxrecordsinram", submodule = "picard")
var maxRecordsInRam: Option[Int] = config("maxrecordsinram")
@Argument(doc = "CREATE_INDEX", required = false)
var createIndex: Boolean = config("createindex", default = true, submodule = "picard")
var createIndex: Boolean = config("createindex", default = true)
@Argument(doc = "CREATE_MD5_FILE", required = false)
var createMd5: Boolean = config("createmd5", default = false, submodule = "picard")
var createMd5: Boolean = config("createmd5", default = false)
// override def versionCommand = executable + " " + javaOpts + " " + javaExecutable + " -h"
// override val versionRegex = """Version: (.*)""".r
......
......@@ -21,7 +21,9 @@ abstract class Sambamba extends BiopetCommandLineFunction {
override val defaultVmem = "4G"
override val defaultThreads = 2
executable = config("exe", default = "sambamba", submodule = "sambamba", freeVar = false)
override def subPath = "sambamba" :: super.subPath
executable = config("exe", default = "sambamba", freeVar = false)
override def versionCommand = executable
override val versionRegex = """sambamba v(.*)""".r
override val versionExitcode = List(0, 1)
......
......@@ -18,7 +18,8 @@ package nl.lumc.sasc.biopet.extensions.samtools
import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
abstract class Samtools extends BiopetCommandLineFunction {
executable = config("exe", default = "samtools", submodule = "samtools", freeVar = false)
override def subPath = "samtools" :: super.subPath
executable = config("exe", default = "samtools", freeVar = false)
override def versionCommand = executable
override val versionRegex = """Version: (.*)""".r
override val versionExitcode = List(0, 1)
......
......@@ -21,7 +21,8 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
* Abstract class for all seqtk wrappers.
*/
abstract class Seqtk extends BiopetCommandLineFunction {
executable = config("exe", default = "seqtk", submodule = "seqtk")
override def subPath = "seqtk" :: super.subPath
executable = config("exe", default = "seqtk", freeVar = true)
override def versionCommand = executable
override val versionRegex = """Version: (.*)""".r
override val versionExitcode = List(0, 1)
......
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