Commit 133cd485 authored by bow's avatar bow
Browse files

Force version retrieval and path resolution in CustomVarscan

parent 81e0124f
......@@ -66,7 +66,10 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
require(output.toString.endsWith(".gz"), "Output must have a .gz file extension")
}
def cmdLine: String =
def cmdLine: String = {
// FIXME: manual trigger of commandLine for version retrieval
mpileup.commandLine
mpileup.cmdPipe + " | " + fixMpileup.commandLine + " | " + removeEmptyPile.commandLine + " | " +
varscan.commandLine + " | " + compress.commandLine + " && " + index.commandLine
}
}
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