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Commit d7e3156a authored by Peter van 't Hof's avatar Peter van 't Hof
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Fix reference name

parent ef67b6a8
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Showing with 9 additions and 9 deletions
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @ d7e3156a
......@@ -37,8 +37,8 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
gatkPipeline.biopetScript
addAll(gatkPipeline.functions)
val refVariants = addGenerateFasta(null, outputDir + "reference/", "reference")
val refVariantSnps = addGenerateFasta(null, outputDir + "reference/", "reference", snpsOnly = true)
val refVariants = addGenerateFasta(null, outputDir + "reference/", outputName = "reference")
val refVariantSnps = addGenerateFasta(null, outputDir + "reference/", outputName = "reference", snpsOnly = true)
runSamplesJobs()
......@@ -105,8 +105,8 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
sampleOutput.libraries = runLibraryJobs(sampleConfig)
sampleOutput.output = addGenerateFasta(sampleID, sampleDir, sampleID)
sampleOutput.outputSnps = addGenerateFasta(sampleID, sampleDir, sampleID, snpsOnly = true)
sampleOutput.output = addGenerateFasta(sampleID, sampleDir)
sampleOutput.outputSnps = addGenerateFasta(sampleID, sampleDir, snpsOnly = true)
return sampleOutput
}
......@@ -122,18 +122,18 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
return libraryOutput
}
def addGenerateFasta(sampleName: String, outputDir: String, outputName: String,
def addGenerateFasta(sampleName: String, outputDir: String, outputName: String = null,
snpsOnly: Boolean = false): FastaOutput = {
val bastyGenerateFasta = new BastyGenerateFasta(this)
bastyGenerateFasta.outputName = if (outputName != null) outputName else sampleName
bastyGenerateFasta.inputVcf = gatkPipeline.multisampleVariantcalling.scriptOutput.finalVcfFile
if (gatkPipeline.samplesOutput.contains(sampleName)) {
bastyGenerateFasta.bamFile = gatkPipeline.samplesOutput(sampleName).variantcalling.bamFiles.head
}
bastyGenerateFasta.outputVariants = outputDir + sampleName + ".variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta"
bastyGenerateFasta.outputConsensus = outputDir + sampleName + ".consensus" + (if (snpsOnly) ".snps_only" else "") + ".fasta"
bastyGenerateFasta.outputConsensusVariants = outputDir + sampleName + ".consensus_variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta"
bastyGenerateFasta.outputVariants = outputDir + bastyGenerateFasta.outputName + ".variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta"
bastyGenerateFasta.outputConsensus = outputDir + bastyGenerateFasta.outputName + ".consensus" + (if (snpsOnly) ".snps_only" else "") + ".fasta"
bastyGenerateFasta.outputConsensusVariants = outputDir + bastyGenerateFasta.outputName + ".consensus_variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta"
bastyGenerateFasta.sampleName = sampleName
bastyGenerateFasta.outputName = if (outputName != null) outputName else sampleName
bastyGenerateFasta.snpsOnly = snpsOnly
add(bastyGenerateFasta)
return FastaOutput(bastyGenerateFasta.outputVariants, bastyGenerateFasta.outputConsensus, bastyGenerateFasta.outputConsensusVariants)
......
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