Fixed RepSet

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/qiime/PickRepSet.scala

@@ -24,7 +24,9 @@ class PickRepSet(val root: Configurable) extends BiopetCommandLineFunction with
   @Input(required = false)
   var reference_seqs_fp: Option[File] = config("reference_seqs_fp")
 
-  var outputDir: File = _
+  @Input(required = false)
+  var fastaInput: Option[File] = None
+
   var sortBy: Option[String] = config("sort_by")
 
   def versionCommand = executable + " --version"
@@ -34,9 +36,9 @@ class PickRepSet(val root: Configurable) extends BiopetCommandLineFunction with
 
   def cmdLine = executable +
     required("-i", inputFile) +
-    optional("-f", outputFasta) +
+    required("-o", outputFasta) +
     optional("-m", rep_set_picking_method) +
-    required("-o", outputDir) +
+    optional("-f", fastaInput) +
     optional("-l", logFile) +
     optional("-s", sortBy) +
     optional("-r", reference_seqs_fp)

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeRtax.scala

@@ -38,10 +38,10 @@ class GearsQiimeRtax(val root: Configurable) extends QScript with BiopetQScript
     add(pickOtus)
 
     val pickRepSet = new PickRepSet(this)
-    pickRepSet.outputDir = new File(outputDir, "pick_rep_set")
+    val repSetOutputDir = new File(outputDir, "pick_rep_set")
     pickRepSet.inputFile = pickOtus.otusTxt
-    pickRepSet.outputFasta = Some(new File(pickRepSet.outputDir, fastaR1.getName))
-    pickRepSet.logFile = Some(new File(pickRepSet.outputDir, fastaR1.getName
+    pickRepSet.outputFasta = Some(new File(repSetOutputDir, fastaR1.getName))
+    pickRepSet.logFile = Some(new File(repSetOutputDir, fastaR1.getName
       .stripSuffix(".fasta").stripSuffix(".fa").stripSuffix(".fna") + ".log"))
     add(pickRepSet)