Commit c340b559 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

changed version command to def

parent 07c486e9
......@@ -18,6 +18,8 @@ class Cutadapt(val root:Configurable) extends BiopetCommandLineFunction {
var fastq_output: File = _
executeble = config("exe","cutadapt")
override def versionCommand = executeble + " --version"
override val versionRegex = """(.*)""".r
var default_clip_mode:String = config("default_clip_mode", "3")
var opt_adapter: Set[String] = config("adapter", Nil)
......@@ -27,15 +29,9 @@ class Cutadapt(val root:Configurable) extends BiopetCommandLineFunction {
var opt_discard: Boolean = config("discard",false)
var opt_minimum_length: String = config("minimum_length", 1)
var opt_maximum_length: String = config("maximum_length", null)
override val versionRegex = """(.*)""".r
override def afterGraph() {
versionCommand = executeble + " --version"
}
override def beforeCmd() {
this.getContamsFromFile
getContamsFromFile
}
def cmdLine = {
......
......@@ -31,9 +31,10 @@ class Fastqc(val root:Configurable) extends BiopetCommandLineFunction {
this.checkExecuteble
val fastqcDir = executeble.substring(0, executeble.lastIndexOf("/"))
if (contaminants == null) contaminants = new File(fastqcDir + "/Contaminants/contaminant_list.txt")
versionCommand = executeble + " --version"
}
override def versionCommand = executeble + " --version"
def cmdLine = {
required(executeble) +
optional("--java", java_exe) +
......
......@@ -38,10 +38,10 @@ class Sickle(val root:Configurable) extends BiopetCommandLineFunction {
override def afterGraph {
if (defaultQualityType == null) defaultQualityType = config("defaultqualitytype", "sanger")
if (qualityType == null && defaultQualityType != null) qualityType = defaultQualityType
versionCommand = executeble + " --version"
}
override def versionCommand = executeble + " --version"
override def beforeCmd {
qualityType = getQualityTypeFromFile
}
......
......@@ -19,18 +19,17 @@ class Bwa(val root:Configurable) extends BiopetCommandLineFunction {
@Output(doc="Output file SAM", shortName="output")
var output: File = _
executeble = config("exe", "bwa")
var RG: String = _
var M: Boolean = config("M", true)
executeble = config("exe", "bwa")
override val versionRegex = """Version: (.*)""".r
override val versionExitcode = List(0,1)
override val defaultVmem = "6G"
override val defaultThreads = 8
override val versionRegex = """Version: (.*)""".r
override def beforeCmd() {
versionCommand = executeble
}
override def versionCommand = executeble
def cmdLine = {
required(executeble) +
......
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