Commit bfa58fe2 authored by bow's avatar bow
Browse files

Fix wrong threads setting in Star wrapper

parent eff9c5cd
......@@ -61,6 +61,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
var runmode: String = _
var sjdbOverhang: Int = _
var outFileNamePrefix: String = _
var runThreadN: Option[Int] = config("runThreadN")
override val defaultVmem = "6G"
override val defaultThreads = 8
......@@ -79,6 +80,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
outputSAindex = new File(prefix + "SAindex")
sjdbOverhang = config("sjdboverhang", 75)
}
threads = runThreadN.getOrElse(1)
}
/** Returns command to execute */
......@@ -92,7 +94,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction {
}
cmd += required("--genomeDir", genomeDir) +
optional("--sjdbFileChrStartEnd", sjdbFileChrStartEnd) +
optional("--runThreadN", nCoresRequest) +
optional("--runThreadN", threads) +
optional("--outFileNamePrefix", outFileNamePrefix)
if (sjdbOverhang > 0) cmd += optional("--sjdbOverhang", sjdbOverhang)
......
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