Commit 3828a150 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change arg to multiarg

parent a8748725
......@@ -40,8 +40,8 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
@Output(doc = "Output tab file", required = false)
var outputTab: File = _
@Input(doc = "sjdbFileChrStartEnd file", required = false) /**Can be a list of file Paths TO BE CHECKED **/
var sjdbFileChrStartEnd: File = _
@Input(doc = "sjdbFileChrStartEnd file", required = false)
var sjdbFileChrStartEnd: List[File] = Nil
@Output(doc = "Output genome file", required = false)
var outputGenome: File = _
......@@ -237,7 +237,7 @@ class Star(val root: Configurable) extends BiopetCommandLineFunction with Refere
cmd += required("--readFilesIn", R1) + optional(R2)
}
cmd += required("--genomeDir", genomeDir) +
optional("--sjdbFileChrStartEnd", sjdbFileChrStartEnd) +
multiArg("--sjdbFileChrStartEnd", sjdbFileChrStartEnd) +
optional("--runThreadN", threads) +
optional("--outFileNamePrefix", outFileNamePrefix) +
optional("--sjdbOverhang", sjdbOverhang) +
......@@ -420,7 +420,7 @@ object Star {
starCommandPass1.beforeGraph()
val starCommandReindex = new Star(configurable)
starCommandReindex.sjdbFileChrStartEnd = starCommandPass1.outputTab
starCommandReindex.sjdbFileChrStartEnd :+= starCommandPass1.outputTab
starCommandReindex.outputDir = new File(outputDir, "re-index")
starCommandReindex.runmode = "genomeGenerate"
starCommandReindex.isIntermediate = isIntermediate
......
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