Commit dbab1a53 authored by bow's avatar bow
Browse files

Fix wrong threads setting in GSNAP wrapper

parent e76f0625
......@@ -326,6 +326,10 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
override val versionRegex = """.* version (.*)""".r
override def versionCommand = executable + " --version"
override def beforeGraph: Unit = {
threads = nthreads.getOrElse(1)
}
def cmdLine = {
required(executable) +
optional("--dir", dir) +
......@@ -371,7 +375,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
optional("--use-tally", use_tally) +
optional("--runlengthdir", runlengthdir) +
optional("--use-runlength", use_runlength) +
optional("--nthreads", nCoresRequest) +
optional("--nthreads", threads) +
optional("--gmap-mode", gmap_mode) +
optional("--trigger-score-for-gmap", trigger_score_for_gmap) +
optional("--gmap-min-match-length", gmap_min_match_length) +
......
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