Commit 46cef440 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge branch 'patch-aln_wrapper_threads' into 'develop'

Patch aln wrapper threads

@p.j.van_t_hof, @wyleung, and @a.h.b.bollen ~ for the threads behavior that we saw earlier today

See merge request !124
parents 354ea985 bfa58fe2
......@@ -61,7 +61,7 @@ class Bowtie(val root: Configurable) extends BiopetCommandLineFunction {
/** return commandline to execute */
def cmdLine = {
required(executable) +
optional("--threads", nCoresRequest) +
optional("--threads", threads) +
conditional(sam, "--sam") +
conditional(best, "--best") +
conditional(strata, "--strata") +
......
......@@ -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)
......
......@@ -51,6 +51,7 @@ class BwaAln(val root: Configurable) extends Bwa {
/** Returns command to execute */
def cmdLine = required(executable) +
required("aln") +
optional("-t", threads) +
optional("-n", n) +
optional("-o", o) +
optional("-e", e) +
......
......@@ -77,7 +77,7 @@ class BwaMem(val root: Configurable) extends Bwa {
required("mem") +
optional("-k", k) +
optional("-r", r) +
optional("-t", nCoresRequest) +
optional("-t", threads) +
optional("-R", R) +
conditional(M, "-M") +
conditional(S, "-S") +
......
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