From 1062e3abdc14421ad6613187875c8ab220a2c1ba Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 16 Feb 2015 19:33:31 +0100
Subject: [PATCH] Fix output dirs and set default single sample calling off
---
.../sasc/biopet/pipelines/basty/Basty.scala | 19 ++++++++++---------
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
index 544af1b7c..506b3433e 100644
--- a/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+++ b/protected/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
@@ -25,7 +25,8 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
"ploidy" -> 1,
"use_haplotypecaller" -> false,
"use_unifiedgenotyper" -> true,
- "joint_variantcalling" -> true
+ "joint_variantcalling" -> true,
+ "single_sample_calling" -> false
), super.defaults)
var gatkPipeline: GatkPipeline = new GatkPipeline(qscript)
@@ -60,8 +61,8 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
}
def addMultiSampleJobs(): Unit = {
- val refVariants = addGenerateFasta(null, new File(outputDir, "reference"), outputName = "reference")
- val refVariantSnps = addGenerateFasta(null, new File(outputDir, "reference"), outputName = "reference", snpsOnly = true)
+ val refVariants = addGenerateFasta(null, new File(outputDir, "fastas" + File.separator + "reference"), outputName = "reference")
+ val refVariantSnps = addGenerateFasta(null, new File(outputDir, "fastas" + File.separator + "reference"), outputName = "reference", snpsOnly = true)
val catVariants = Cat(this, refVariants.variants :: samples.map(_._2.output.variants).toList,
new File(outputDir, "fastas" + File.separator + "variant.fasta"))
@@ -94,7 +95,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
raxmlMl.m = config("raxml_ml_model", default = "GTRGAMMAX")
raxmlMl.p = seed
raxmlMl.n = outputName + "_ml"
- raxmlMl.w = outputDir + dirSufixRaxml
+ raxmlMl.w = dirSufixRaxml
raxmlMl.N = config("ml_runs", default = 20, submodule = "raxml")
add(raxmlMl)
@@ -114,7 +115,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
raxmlBoot.getBootstrapFile
}
- val cat = Cat(this, bootList.toList, outputDir + "/boot_list")
+ val cat = Cat(this, bootList.toList, new File(outputDir, "/boot_list"))
add(cat)
val raxmlBi = new Raxml(this)
@@ -125,7 +126,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
raxmlBi.p = seed
raxmlBi.f = "b"
raxmlBi.n = outputName + "_bi"
- raxmlBi.w = outputDir + dirSufixRaxml
+ raxmlBi.w = dirSufixRaxml
add(raxmlBi)
val gubbins = new RunGubbins(this)
@@ -150,9 +151,9 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
if (gatkPipeline.samples.contains(sampleName)) {
bastyGenerateFasta.bamFile = gatkPipeline.samples(sampleName).gatkVariantcalling.scriptOutput.bamFiles.head
}
- 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.outputVariants = new File(outputDir, bastyGenerateFasta.outputName + ".variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta")
+ bastyGenerateFasta.outputConsensus = new File(outputDir, bastyGenerateFasta.outputName + ".consensus" + (if (snpsOnly) ".snps_only" else "") + ".fasta")
+ bastyGenerateFasta.outputConsensusVariants = new File(outputDir, bastyGenerateFasta.outputName + ".consensus_variants" + (if (snpsOnly) ".snps_only" else "") + ".fasta")
bastyGenerateFasta.sampleName = sampleName
bastyGenerateFasta.snpsOnly = snpsOnly
qscript.add(bastyGenerateFasta)
--
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