Changed name in extension

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/DownloadNcbiAssembly.scala

@@ -31,7 +31,8 @@ class DownloadNcbiAssembly(val root: Configurable) extends ToolCommandFunction {
 
   var outputReport: File = _
 
-  var assemblyId: String = null
+  @Input(required = true)
+  var assemblyReport: File = null
 
   var nameHeader: Option[String] = None
 
@@ -41,7 +42,7 @@ class DownloadNcbiAssembly(val root: Configurable) extends ToolCommandFunction {
   override def defaultCoreMemory = 4.0
 
   override def cmdLine = super.cmdLine +
-    required("-a", assemblyId) +
+    required("-a", assemblyReport) +
     required("--report", outputReport) +
     required("-o", output) +
     optional("--nameHeader", nameHeader) +

generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/DownloadGenomes.scala

@@ -65,9 +65,9 @@ class DownloadGenomes(val root: Configurable) extends QScript with BiopetQScript
         val downloadFastaFile = new File(genomeDir, "download.reference.fa")
 
         genomeConfig.get("ncbi_assembly_report") match {
-          case Some(assemblyID: String) =>
+          case Some(assemblyReport: String) =>
             val downloadAssembly = new DownloadNcbiAssembly(this)
-            downloadAssembly.assemblyId = assemblyID
+            downloadAssembly.assemblyReport = new File(assemblyReport)
             downloadAssembly.output = downloadFastaFile
             downloadAssembly.outputReport = new File(genomeDir, s"$speciesName-$genomeName.assembly.report")
             downloadAssembly.nameHeader = genomeConfig.get("ncbi_assembly_header_name").map(_.toString)