From d7e3156aad422e15f2a49e1b98f1aa957e2736be Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 17 Nov 2014 06:58:52 +0100
Subject: [PATCH] Fix reference name
---
.../sasc/biopet/pipelines/basty/Basty.scala | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
index 3f847b096..9e73788f7 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
@@ -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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