Commit 57622630 authored by bow's avatar bow
Browse files

Fix wrong threads setting in TopHat wrapper

parent dbab1a53
......@@ -266,6 +266,10 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
var rg_platform: Option[String] = config("rg_platform")
override def beforeGraph: Unit = {
threads = num_threads.getOrElse(1)
}
def cmdLine: String = required(executable) +
optional("-o", output_dir) +
conditional(bowtie1, "--bowtie1") +
......@@ -291,7 +295,7 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
conditional(color, "--color") +
conditional(color_out, "--color-out") +
optional("--library-type", library_type) +
optional("--num-threads", num_threads) +
optional("--num-threads", threads) +
optional("--resume", resume) +
optional("--GTF", GTF) +
optional("--transcriptome-index", transcriptome_index) +
......
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