Commit 8ab8f962 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

fix some code warnings

parent f737d360
......@@ -94,7 +94,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
def commandLine = cmds.mkString(" && ")
}
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)
......@@ -159,14 +159,13 @@ 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")
}
}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment