Commit e749d3ed authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix tool extensions

parent 48528ed5
......@@ -6,5 +6,12 @@ import nl.lumc.sasc.biopet.FullVersion
* Created by pjvanthof on 11/09/15.
*/
trait ToolCommandFuntion extends BiopetJavaCommandLineFunction {
def toolObject: Object
override def getVersion = Some("Biopet " + FullVersion)
override def freezeFieldValues(): Unit = {
javaMainClass = toolObject.getClass.getName.split("$").head
super.freezeFieldValues()
}
}
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with Reference {
javaMainClass = nl.lumc.sasc.biopet.tools.BastyGenerateFasta.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.BastyGenerateFasta
@Input(doc = "Input vcf file", required = false)
var inputVcf: File = _
......
......@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* @deprecated Use picard.util.BedToIntervalList instead
*/
class BedToInterval(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.BedToInterval.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.BedToInterval
@Input(doc = "Input Bed file", required = true)
var input: File = _
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts
@Input(doc = "Input fasta", shortName = "input", required = true)
var input: File = _
......
......@@ -24,7 +24,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
javaMainClass = nl.lumc.sasc.biopet.tools.BiopetFlagstat.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.BiopetFlagstat
@Input(doc = "Input bam", shortName = "input", required = true)
var input: File = _
......
......@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* @param root Parent object
*/
class FastqSplitter(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.FastqSplitter.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.FastqSplitter
@Input(doc = "Input fastq", shortName = "input", required = true)
var input: File = _
......
......@@ -32,7 +32,7 @@ import scala.util.matching.Regex
*/
class FastqSync(val root: Configurable) extends ToolCommandFuntion with Summarizable {
javaMainClass = nl.lumc.sasc.biopet.tools.FastqSync.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.FastqSync
@Input(doc = "Original FASTQ file (read 1 or 2)", shortName = "r", required = true)
var refFastq: File = null
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.MergeAlleles.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.MergeAlleles
@Input(doc = "Input vcf files", shortName = "input", required = true)
var input: List[File] = Nil
......
......@@ -30,7 +30,7 @@ import scala.collection.mutable.{ Set => MutSet }
*/
class MergeTables(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.MergeTables.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.MergeTables
override def defaultCoreMemory = 6.0
......
......@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Reference {
javaMainClass = nl.lumc.sasc.biopet.tools.MpileupToVcf.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.MpileupToVcf
@Input(doc = "Input mpileup file", shortName = "mpileup", required = false)
var inputMpileup: File = _
......
......@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
* Created by pjvan_thof on 1/13/15.
*/
class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.PrefixFastq.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.PrefixFastq
override def defaultCoreMemory = 1.0
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.SageCountFastq.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.SageCountFastq
@Input(doc = "Input fasta", shortName = "input", required = true)
var input: File = _
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.SageCreateLibrary.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.SageCreateLibrary
@Input(doc = "Input fasta", shortName = "input", required = true)
var input: File = _
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.SageCreateTagCounts.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.SageCreateTagCounts
@Input(doc = "Raw count file", shortName = "input", required = true)
var input: File = _
......
......@@ -14,7 +14,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
* @param root Configuration object for the pipeline
*/
class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
javaMainClass = nl.lumc.sasc.biopet.tools.SeqStat.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.SeqStat
@Input(doc = "Input FASTQ", shortName = "input", required = true)
var input: File = null
......
......@@ -10,7 +10,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* Created by pjvanthof on 22/08/15.
*/
class SquishBed(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.SquishBed.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.SquishBed
@Input(doc = "Input Bed file", required = true)
var input: File = _
......
......@@ -22,7 +22,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.VcfFilter.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.VcfFilter
@Input(doc = "Input vcf", shortName = "I", required = true)
var inputVcf: File = _
......
......@@ -30,7 +30,7 @@ import scala.io.Source
* Created by pjvan_thof on 1/10/15.
*/
class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summarizable with Reference {
javaMainClass = nl.lumc.sasc.biopet.tools.VcfStats.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.VcfStats
@Input(doc = "Input fastq", shortName = "I", required = true)
var input: File = _
......
......@@ -25,7 +25,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
* Biopet extension for tool VcfWithVcf
*/
class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.VcfWithVcf.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.VcfWithVcf
@Input(doc = "Input vcf file", shortName = "input", required = true)
var input: File = _
......
......@@ -32,7 +32,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
*/
class VepNormalizer(val root: Configurable) extends ToolCommandFuntion {
javaMainClass = nl.lumc.sasc.biopet.tools.VepNormalizer.getClass.getName
def toolObject = nl.lumc.sasc.biopet.tools.VepNormalizer
@Input(doc = "Input VCF, may be indexed", shortName = "InputFile", required = true)
var inputVCF: File = null
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment