From 54d818a20a1c9eebfdf5b15762504d5967648708 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 12 Nov 2014 15:35:39 +0100
Subject: [PATCH] Changed Queue wrapper
---
.../biopet/tools/BastyGenerateFasta.scala | 25 +++++++++++++------
1 file changed, 17 insertions(+), 8 deletions(-)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
index 24d05acea..641896648 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
@@ -9,7 +9,7 @@ import java.io.PrintWriter
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
import scala.collection.JavaConversions._
import nl.lumc.sasc.biopet.util.VcfUtils._
@@ -22,30 +22,39 @@ class BastyGenerateFasta(val root: Configurable) extends BiopetJavaCommandLineFu
@Input(doc = "Bam File", required = false)
var bamFile: File = _
+ @Input(doc = "reference", required = false)
+ var reference: File = config("reference")
+
@Output(doc = "Output fasta, variants only", required = false)
var outputVariants: File = _
- @Argument(doc = "Output interval list", required = false)
- var snpsOnly: Boolean = config("snps_only", default = false)
+ @Output(doc = "Output fasta, variants only", required = false)
+ var outputConsensus: File = _
- @Argument(doc = "Sample name", required = false)
- var sampleName: String = _
+ @Output(doc = "Output fasta, variants only", required = false)
+ var outputConsensusVariants: File = _
- @Argument(doc = "minAD", required = false)
+ var snpsOnly: Boolean = config("snps_only", default = false)
+ var sampleName: String = _
var minAD: Int = config("min_ad", default = 8)
+ var minDepth: Int = config("min_depth", default = 8)
+ var outputName: String = _
override val defaultVmem = "8G"
memoryLimit = Option(4.0)
- var reference = false
override def commandLine = super.commandLine +
optional("--inputVcf", inputVcf) +
optional("--bamFile", bamFile) +
optional("--outputVariants", outputVariants) +
+ optional("--outputVariants", outputConsensus) +
+ optional("--outputVariants", outputConsensusVariants) +
conditional(snpsOnly, "--snpsOnly") +
optional("--sampleName", sampleName) +
+ required("--outputName", outputName) +
optional("--minAD", minAD) +
- conditional(reference, "--reference")
+ optional("--minDepth", minDepth) +
+ optional("--reference", reference)
}
object BastyGenerateFasta extends ToolCommand {
--
GitLab