From 0801801133d8771442e22f987abfb23f18c40981 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sun, 8 Mar 2015 23:02:18 +0100
Subject: [PATCH] Use correct threads and mem values for Cufflinks and Gsnap
wrapper
---
.../scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala | 6 +++---
.../main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala | 6 +++---
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
index cc9b0490c..31aa485a5 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
@@ -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) +
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
index a518e7246..efcb7fe13 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
@@ -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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