From 7d08761a0341235b2e4475bebf867169a9760ba4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 10 Jun 2014 17:43:19 +0200
Subject: [PATCH] Added outFileNamePrefix option
---
.../sasc/biopet/wrappers/aligners/Star.scala | 20 +++++++++++--------
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala b/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
index 06f4d4371..54e2928fc 100644
--- a/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
+++ b/mapping/src/main/java/nl/lumc/sasc/biopet/wrappers/aligners/Star.scala
@@ -23,6 +23,7 @@ class Star(val globalConfig: Config) extends CommandLineFunction {
@Output(doc="Output tab file", required=false) var outputTab: File = _
@Input(doc="sjdbFileChrStartEnd file", required=false) var sjdbFileChrStartEnd: File = _
@Argument(doc="sjdbOverhang", required=false) var sjdbOverhang: Int = _
+ @Argument(doc="outFileNamePrefix", required=false) var outFileNamePrefix: String = _
@Input(doc="deps", required=false) var deps: List[File] = Nil
@Output(doc="Output genome file", required=false) var outputGenome: File = _
@@ -31,17 +32,20 @@ class Star(val globalConfig: Config) extends CommandLineFunction {
jobResourceRequests :+= "h_vmem=" + config.getAsString("vmem", "6G")
nCoresRequest = Option(config.getThreads(8))
+ addJobReportBinding("version", "NA")
def init() {
- this.addJobReportBinding("version", "NA")
+ if (outFileNamePrefix != null && !outFileNamePrefix.endsWith(".")) outFileNamePrefix +="."
+ if (!outputDir.endsWith("/")) outputDir += "/"
+ val prefix = if (outFileNamePrefix != null) outputDir+outFileNamePrefix else outputDir
if (runmode == null) {
- outputSam = new File(outputDir + "/Aligned.out.sam")
- outputTab = new File(outputDir + "/SJ.out.tab")
+ outputSam = new File(prefix + "Aligned.out.sam")
+ outputTab = new File(prefix + "SJ.out.tab")
} else if (runmode == "genomeGenerate") {
genomeDir = outputDir
- outputGenome = new File(genomeDir + "/Genome")
- outputSA = new File(genomeDir + "/SA")
- outputSAindex = new File(genomeDir + "/SAindex")
+ outputGenome = new File(prefix + "Genome")
+ outputSA = new File(prefix + "SA")
+ outputSAindex = new File(prefix + "SAindex")
}
}
@@ -50,14 +54,14 @@ class Star(val globalConfig: Config) extends CommandLineFunction {
var cmd: String = required("cd",outputDir) + "&&" + required(star_exe)
if (runmode != null && runmode == "genomeGenerate") { // Create index
cmd += required("--runMode", runmode) +
- //required("--genomeDir", genomeDir) +
required("--genomeFastaFiles", referenceFile)
} else { // Aligner
cmd += required("--readFilesIn", R1) + optional(R2)
}
cmd += required("--genomeDir", genomeDir) +
optional("--sjdbFileChrStartEnd", sjdbFileChrStartEnd) +
- optional("--runThreadN", nCoresRequest)
+ optional("--runThreadN", nCoresRequest) +
+ optional("--outFileNamePrefix", outFileNamePrefix)
if (sjdbOverhang > 0) cmd += optional("--sjdbOverhang", sjdbOverhang)
return cmd
--
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