Commit 8b63b1b7 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed code warnings

parent 1ab86824
......@@ -87,7 +87,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
val fastaCat = new FastaMerging(this)
fastaCat.output = fastaFile
if (fastaUris.length > 1 || fastaFiles.filter(_.getName.endsWith(".gz")).nonEmpty) {
if (fastaUris.length > 1 || fastaFiles.exists(_.getName.endsWith(".gz"))) {
fastaFiles.foreach { file =>
if (file.getName.endsWith(".gz")) {
val zcat = new Zcat(this)
......@@ -152,14 +152,13 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
val regex = """.*\/(.*)_vep_(\d*)_(.*)\.tar\.gz""".r
vepCacheUri.toString match {
case regex(species, version, assembly) if (version.forall(_.isDigit)) => {
case regex(species, version, assembly) if version.forall(_.isDigit) =>
outputConfig ++= Map("varianteffectpredictor" -> Map(
"species" -> species,
"assembly" -> assembly,
"cache_version" -> version.toInt,
"cache" -> vepDir,
"fasta" -> createLinks(vepDir)))
}
case _ => throw new IllegalArgumentException("Cache found but no version was found")
}
}
......
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