Commit 6f001daf authored by Peter van 't Hof's avatar Peter van 't Hof

Added allele index to deps

parent 26fa9924
......@@ -411,7 +411,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
if (bamOutput != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(bamOutput))
if (generate_md5)
bamOutputMD5 = new File(bamOutput.getPath + ".md5")
alleles.foreach(VcfUtils.getVcfIndexFile(_))
alleles.foreach(deps :+= VcfUtils.getVcfIndexFile(_))
num_cpu_threads_per_data_thread = Some(getThreads)
}
......
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