Commit 711d36a4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding validation

parent 729f76ee
......@@ -82,8 +82,12 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
/** This will add jobs for this pipeline */
def biopetScript(): Unit = {
require(inputBams.nonEmpty, "No input bams found")
require(callers.nonEmpty, "must select at least 1 variantcaller, choices are: " + ShivaVariantcalling.callersList(this).map(_.name).mkString(", "))
if (inputBams.isEmpty) {
Logging.addError("No input bams found")
inputBams = Map("test", new File("."))
}
if (callers.isEmpty) Logging.addError("must select at least 1 variantcaller, choices are: " + ShivaVariantcalling.callersList(this).map(_.name).mkString(", "))
if (!callers.exists(_.mergeVcfResults)) Logging.addError("must select at least 1 variantcaller where merge_vcf_results is true")
addAll(dbsnpVcfFile.map(Shiva.makeValidateVcfJobs(this, _, referenceFasta(), new File(outputDir, ".validate"))).getOrElse(Nil))
......
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