Commit 6cb4dcbe authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added index to vt jobs

parent 050af98d
......@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.Tabix
import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordance }
import nl.lumc.sasc.biopet.extensions.tools.VcfStats
import nl.lumc.sasc.biopet.extensions.vt.{ VtDecompose, VtNormalize }
......@@ -101,19 +102,19 @@ trait ShivaVariantcallingTrait extends SummaryQScript
if (normalize && decompose) {
vtNormalize.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".normaize.vcf.gz")
vtNormalize.isIntermediate = true
add(vtNormalize)
add(vtNormalize, Tabix(this, vtNormalize.outputVcf))
vtDecompose.inputVcf = vtNormalize.outputVcf
vtDecompose.outputVcf = swapExt(caller.outputDir, vtNormalize.outputVcf, ".vcf.gz", ".decompose.vcf.gz")
add(vtDecompose)
add(vtDecompose, Tabix(this, vtDecompose.outputVcf))
cv.addInput(vtDecompose.outputVcf, caller.name)
} else if (normalize && !decompose) {
vtNormalize.outputVcf = swapExt(caller.outputDir, caller.outputFile, ".vcf.gz", ".normaize.vcf.gz")
add(vtNormalize)
add(vtNormalize, Tabix(this, vtNormalize.outputVcf))
cv.addInput(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)
add(vtDecompose, Tabix(this, vtDecompose.outputVcf))
cv.addInput(vtDecompose.outputVcf, caller.name)
} else cv.addInput(caller.outputFile, caller.name)
}
......
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