Commit 532f837c authored by pjvan_thof's avatar pjvan_thof
Browse files

Adding default gtf file to STAR

parent 250e63be
......@@ -80,8 +80,13 @@ class Star(val parent: Configurable)
var genomeSAindexNbases: Option[Long] = config("genomesaindexnbases")
var genomeSAsparseD: Option[Int] = config("genomesasparsed")
val defaultGtf: Option[File] = config("annotation_gtf")
@Input(required = false)
var sjdbGTFfile: Option[File] = config("sjdbgtfile")
var sjdbGTFfile: Option[File] = defaultGtf match {
case Some(file) => config("sjdbgtfile", default = file)
case _ => config("sjdbgtfile")
}
var sjdbGTFchrPrefix: Option[String] = config("sjdbgtfchrprefix")
var sjdbGTFfeatureExon: Option[String] = config("sjdbgtffeatureexon")
var sjdbGTFtagExonParentTranscript: Option[String] = config("sjdbgtftagexonparenttranscript")
......
......@@ -31,16 +31,17 @@ object ValidateAnnotation extends ToolCommand {
gtfFiles: List[File] = Nil)
class OptParser extends AbstractOptParser[Args](commandName) {
opt[File]('r', "refflatFile") unbounded() maxOccurs 1 valueName "<file>" action { (x, c) =>
opt[File]('r', "refflatFile") unbounded () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(refflatFile = Some(x))
} text "Refflat file to check"
opt[File]('g', "gtfFile") unbounded() valueName "<file>" action { (x, c) =>
opt[File]('g', "gtfFile") unbounded () valueName "<file>" action { (x, c) =>
c.copy(gtfFiles = x :: c.gtfFiles)
} text "Gtf files to check"
opt[File]('R', "reference") unbounded() required () maxOccurs 1 valueName "<file>" action { (x, c) =>
c.copy(reference = x)
opt[File]('R', "reference") unbounded () required () maxOccurs 1 valueName "<file>" action {
(x, c) =>
c.copy(reference = x)
} text "Reference fasta to check vcf file against"
opt[Unit]("disableFail") unbounded() maxOccurs 1 valueName "<file>" action { (_, c) =>
opt[Unit]("disableFail") unbounded () maxOccurs 1 valueName "<file>" action { (_, c) =>
c.copy(failOnError = false)
} text "Do not fail on error. The tool will still exit when encountering an error, but will do so with exit code 0"
}
......
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