Commit 0d14a49a authored by Peter van 't Hof's avatar Peter van 't Hof

Adding gtf download

parent 142c815a
......@@ -196,6 +196,21 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
outputConfig += "dbsnp" -> cv.out
}
val gtfFile: Option[File] = genomeConfig.get("gtf_uri").map { gtfUri =>
val curl = new Curl(this)
curl.url = gtfUri.toString
curl.output = new File(annotationDir, new File(curl.url).getName)
add(curl)
outputConfig += "annotation_gtf" -> curl.output
curl.output
}
val refFlatFile: Option[File] = gtfFile.map { gtf =>
val refFlat = new File(gtf + ".refFlat")
//TODO: gtf to refFlat conversion
refFlat
}
// Bwa index
val bwaIndex = new BwaIndex(this)
bwaIndex.reference = createLinks(new File(genomeDir, "bwa"))
......
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