Commit 8e414bb6 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing some arguments

parent 0ace30b9
......@@ -17,9 +17,11 @@ package nl.lumc.sasc.biopet.extensions
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.{Version, BiopetCommandLineFunction, Reference}
import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Reference, Version}
import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
import scala.util.matching.Regex
/**
* Extension for STAR
*/
......@@ -28,7 +30,7 @@ class Star(val parent: Configurable)
with Reference
with Version {
@Input(doc = "The reference file for the bam files.", required = false)
var reference: File = null
var reference: File = _
@Input(doc = "Fastq file R1", required = false)
var R1: File = _
......@@ -56,13 +58,13 @@ class Star(val parent: Configurable)
executable = config("exe", "STAR")
def versionCommand = executable + " --version"
def versionRegex = """(.*)""".r
def versionCommand: String = executable + " --version"
def versionRegex: Regex = """(.*)""".r
@Argument(doc = "Output Directory")
var outputDir: File = _
var genomeDir: File = null
var genomeDir: File = _
var runmode: String = _
var outFileNamePrefix: String = _
var runThreadN: Option[Int] = config("runthreadn")
......@@ -75,7 +77,7 @@ class Star(val parent: Configurable)
/** can be a list of strings **/
var genomeChrBinNbits: Option[Int] = config("genomechrbinnbits")
var genomeSAindexNbases: Option[Int] = config("genomesaindexnbases")
var genomeSAindexNbases: Option[Long] = config("genomesaindexnbases")
var genomeSAsparseD: Option[Int] = config("genomesasparsed")
@Input(required = false)
......@@ -97,12 +99,12 @@ class Star(val parent: Configurable)
var clip3pAdapterSeq: Option[String] = config("clip3adapterseq")
var clip3pAdapterMMp: Option[String] = config("clip3adaptermmp")
var clip3pAfterAdapterNbases: Option[Int] = config("clip3afteradapternbases")
var limitGenomeGenerateRAM: Option[Int] = config("limitgenomegenerateram")
var limitIObufferSize: Option[Int] = config("limitiobuffersize")
var limitOutSAMoneReadBytes: Option[Int] = config("limitoutsamonereadbytes")
var limitGenomeGenerateRAM: Option[Long] = config("limitgenomegenerateram")
var limitIObufferSize: Option[Long] = config("limitiobuffersize")
var limitOutSAMoneReadBytes: Option[Long] = config("limitoutsamonereadbytes")
var limitOutSJoneRead: Option[Int] = config("limitoutsjoneread")
var limitOutSJcollapsed: Option[Int] = config("limitoutsjcollapsed")
var limitBAMsortRAM: Option[Int] = config("limitbamsortram")
var limitBAMsortRAM: Option[Long] = config("limitbamsortram")
var limitSjdbInsertNsj: Option[Int] = config("limitsjdbinsertnsj")
var outTmpDir: Option[String] = config("outtmpdir")
......@@ -236,7 +238,7 @@ class Star(val parent: Configurable)
}
/** Returns command to execute */
def cmdLine = {
def cmdLine: String = {
var cmd: String = required("cd", outputDir) + " && " + required(executable)
if (runmode != null && runmode == "genomeGenerate") { // Create index
cmd += required("--runMode", runmode) +
......
......@@ -49,7 +49,7 @@ class Toucan(val parent: Configurable)
@Input(doc = "Input GVCF file", shortName = "gvcf", required = false)
var inputGvcf: Option[File] = None
def outputName = inputVcf.getName.stripSuffix(".vcf.gz")
def outputName: String = inputVcf.getName.stripSuffix(".vcf.gz")
def outputVcf: File = (gonlVcfFile, exacVcfFile) match {
case (Some(_), Some(_)) => new File(outputDir, s"$outputName.vep.normalized.gonl.exac.vcf.gz")
......
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