Commit 53240be8 authored by Peter van 't Hof's avatar Peter van 't Hof

Changed name in extension

parent 2364d858
...@@ -31,7 +31,8 @@ class DownloadNcbiAssembly(val root: Configurable) extends ToolCommandFunction { ...@@ -31,7 +31,8 @@ class DownloadNcbiAssembly(val root: Configurable) extends ToolCommandFunction {
var outputReport: File = _ var outputReport: File = _
var assemblyId: String = null @Input(required = true)
var assemblyReport: File = null
var nameHeader: Option[String] = None var nameHeader: Option[String] = None
...@@ -41,7 +42,7 @@ class DownloadNcbiAssembly(val root: Configurable) extends ToolCommandFunction { ...@@ -41,7 +42,7 @@ class DownloadNcbiAssembly(val root: Configurable) extends ToolCommandFunction {
override def defaultCoreMemory = 4.0 override def defaultCoreMemory = 4.0
override def cmdLine = super.cmdLine + override def cmdLine = super.cmdLine +
required("-a", assemblyId) + required("-a", assemblyReport) +
required("--report", outputReport) + required("--report", outputReport) +
required("-o", output) + required("-o", output) +
optional("--nameHeader", nameHeader) + optional("--nameHeader", nameHeader) +
......
...@@ -65,9 +65,9 @@ class DownloadGenomes(val root: Configurable) extends QScript with BiopetQScript ...@@ -65,9 +65,9 @@ class DownloadGenomes(val root: Configurable) extends QScript with BiopetQScript
val downloadFastaFile = new File(genomeDir, "download.reference.fa") val downloadFastaFile = new File(genomeDir, "download.reference.fa")
genomeConfig.get("ncbi_assembly_report") match { genomeConfig.get("ncbi_assembly_report") match {
case Some(assemblyID: String) => case Some(assemblyReport: String) =>
val downloadAssembly = new DownloadNcbiAssembly(this) val downloadAssembly = new DownloadNcbiAssembly(this)
downloadAssembly.assemblyId = assemblyID downloadAssembly.assemblyReport = new File(assemblyReport)
downloadAssembly.output = downloadFastaFile downloadAssembly.output = downloadFastaFile
downloadAssembly.outputReport = new File(genomeDir, s"$speciesName-$genomeName.assembly.report") downloadAssembly.outputReport = new File(genomeDir, s"$speciesName-$genomeName.assembly.report")
downloadAssembly.nameHeader = genomeConfig.get("ncbi_assembly_header_name").map(_.toString) downloadAssembly.nameHeader = genomeConfig.get("ncbi_assembly_header_name").map(_.toString)
......
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