Commit 16422010 authored by bow's avatar bow
Browse files

Fix threads allocation to GSNAP, TopHat, and Cufflinks wrappers

parent aa8fe3fd
......@@ -67,9 +67,6 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
/** write all output files to this directory [./] */
var output_dir: File = config("output_dir", default = new File("."))
/** number of threads used during analysis [1] */
var num_threads: Option[Int] = config("num_threads")
/** value of random number generator seed [0] */
var seed: Option[Int] = config("seed")
......@@ -191,10 +188,6 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
override def versionCommand = executable
override val versionExitcode = List(0, 1)
override def beforeGraph: Unit = {
threads = num_threads.getOrElse(1)
}
def cmdLine =
required(executable) +
required("--output-dir", output_dir) +
......
......@@ -176,9 +176,6 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
/** use this runlength iit file to resolve concordant multiple results */
var use_runlength: Option[String] = config("use_runlength")
/** number of worker threads */
var nthreads: Option[Int] = config("nthreads")
/** cases to use gmap for complex alignments containing multiple splices or indels */
var gmap_mode: Option[String] = config("gmap_mode")
......
......@@ -134,8 +134,6 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction {
var library_type: Option[String] = config("library_type")
var num_threads: Option[Int] = config("num_threads")
var resume: Option[String] = config("resume")
var GTF: Option[String] = config("GTF")
......@@ -266,10 +264,6 @@ 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") +
......
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