Commit 35813ff9 authored by Sander Bollen's avatar Sander Bollen

cant create manwe config in /tmp dir, since that is node-specific

parent f5409cd1
......@@ -68,8 +68,8 @@ abstract class Manwe extends BiopetCommandLineFunction {
val collectionString = s"COLLECTION_CACHE_SIZE = ${collectionCacheSize.getOrElse(20)}"
val dataString = s"DATA_BUFFER_SIZE = ${dataBufferSize.getOrElse(1048576)}"
val taskString = s"TASK_POLL_WAIT = ${taskPollWait.getOrElse(2)}"
val file = File.createTempFile("manwe_config", ".py")
val file = File.createTempFile("manwe_config", ".py", output.getParentFile)
file.deleteOnExit()
val writer = new PrintWriter(file)
writer.println(urlString)
writer.println(tokenString)
......
......@@ -133,6 +133,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
val bed = new GvcfToBed(this)
bed.inputVcf = x.outputVcf
bed.outputBed = swapExt(outputDir, x.outputVcf, ".vcf.gz", ".bed")
bed.minQuality = minGQ
add(bed)
bed
})
......
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