Commit 993d6b05 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing BIOPET-562

parent cefa43a5
......@@ -112,21 +112,22 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
vtDecompose.inputVcf = vtNormalize.outputVcf
vtDecompose.outputVcf = swapExt(caller.outputDir, vtNormalize.outputVcf, ".vcf.gz", ".decompose.vcf.gz")
add(vtDecompose, Tabix(this, vtDecompose.outputVcf))
cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
if (caller.mergeVcfResults) cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
} else if (normalize && !decompose) {
vtNormalize.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".normalized.vcf.gz")
add(vtNormalize, Tabix(this, vtNormalize.outputVcf))
cv.variant :+= TaggedFile(vtNormalize.outputVcf, caller.name)
if (caller.mergeVcfResults) cv.variant :+= TaggedFile(vtNormalize.outputVcf, caller.name)
} else if (!normalize && decompose) {
vtDecompose.inputVcf = caller.outputFile
vtDecompose.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".decompose.vcf.gz")
add(vtDecompose, Tabix(this, vtDecompose.outputVcf))
cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
} else cv.variant :+= TaggedFile(caller.outputFile, caller.name)
if (caller.mergeVcfResults) cv.variant :+= TaggedFile(vtDecompose.outputVcf, caller.name)
} else if (caller.mergeVcfResults) cv.variant :+= TaggedFile(caller.outputFile, caller.name)
}
if (cv.variant.nonEmpty) {
add(cv)
addStats(finalFile, "final")
}
add(cv)
addStats(finalFile, "final")
addSummaryJobs()
}
......
......@@ -27,6 +27,8 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
var namePrefix: String = _
val mergeVcfResults: Boolean = config("merge_vcf_results", default = true)
/**
* Map of samplename -> (preprocessed) bam file
*/
......
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