Commit c6da35a1 authored by Peter van 't Hof's avatar Peter van 't Hof

User gtf has now higher prio

parent 4e52cfc2
......@@ -219,20 +219,21 @@ class DownloadGenomes(val root: Configurable) extends QScript with BiopetQScript
outputFile
}
val gtfFile: Option[File] = if (gffFile.isDefined) gffFile.map { gff =>
val gffRead = new GffRead(this)
gffRead.input = gff
gffRead.output = swapExt(dir, gff, ".gff", ".gtf")
add(gffRead)
gffRead.output
}
else geneAnnotation.get("gtf_uri").map { gtfUri =>
val outputFile = new File(dir, new File(gtfUri.toString).getName.stripSuffix(".gz"))
val curl = new Curl(this)
curl.url = gtfUri.toString
if (gtfUri.toString.endsWith(".gz")) add(curl | Zcat(this) > outputFile)
else add(curl > outputFile)
outputFile
val gtfFile: Option[File] = geneAnnotation.get("gtf_uri") match {
case Some(gtfUri) =>
val outputFile = new File(dir, new File(gtfUri.toString).getName.stripSuffix(".gz"))
val curl = new Curl(this)
curl.url = gtfUri.toString
if (gtfUri.toString.endsWith(".gz")) add(curl | Zcat(this) > outputFile)
else add(curl > outputFile)
Some(outputFile)
case _ => gffFile.map { gff =>
val gffRead = new GffRead(this)
gffRead.input = gff
gffRead.output = swapExt(dir, gff, ".gff", ".gtf")
add(gffRead)
gffRead.output
}
}
val refFlatFile: Option[File] = gtfFile.map { gtf =>
......
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