Commit 08018011 authored by bow's avatar bow
Browse files

Use correct threads and mem values for Cufflinks and Gsnap wrapper

parent e653337b
......@@ -30,10 +30,10 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "cufflinks")
/** default threads */
override def defaultThreads = num_threads.getOrElse(1)
override val defaultThreads = 8
/** default vmem for cluster jobs */
override def defaultVmem = "4G"
override val defaultVmem = "4G"
/** input file */
@Input(doc = "Input file (SAM or BAM)", required = true)
......@@ -194,7 +194,7 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
def cmdLine =
required(executable) +
required("--output-dir", output_dir) +
optional("--num-threads", num_threads) +
optional("--num-threads", nCoresRequest) +
optional("--seed", seed) +
optional("--GTF", GTF) +
optional("--GTF-guide", GTF_guide) +
......
......@@ -23,10 +23,10 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
executable = config("exe", default = "gsnap", freeVar = false)
/** default threads */
override def defaultThreads = nthreads.getOrElse(1)
override val defaultThreads = 8
/** default vmem for cluster jobs */
override def defaultVmem = "4G"
override val defaultVmem = "4G"
/** input file */
@Input(doc = "Input FASTQ file(s)", required = true) //var input: List[File] = _
......@@ -371,7 +371,7 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
optional("--use-tally", use_tally) +
optional("--runlengthdir", runlengthdir) +
optional("--use-runlength", use_runlength) +
optional("--nthreads", nthreads) +
optional("--nthreads", nCoresRequest) +
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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