--- a/0.2.1/modules/kraken2/classify/main.nf	Thu Jul 07 10:37:59 2022 -0400
+++ b/0.2.1/modules/kraken2/classify/main.nf	Mon Jul 11 12:19:48 2022 -0400
@@ -28,15 +28,15 @@
     def readList = reads.collect{ it.toString() }
     def is_single_end = (meta.single_end || meta.is_assembly) ? true : false
     def paired = is_single_end ? "" : "--paired"
-    def classified = is_single_end ? "${prefix}.classified.fastq" : "${prefix}.classified#.fastq"
-    def unclassified = is_single_end ? "${prefix}.unclassified.fastq" : "${prefix}.unclassified#.fastq"
+    def classified = is_single_end ? "--classified-out ${prefix}.classified.fastq" : "--classified-out ${prefix}.classified#.fastq"
+    def unclassified = is_single_end ? "--unclassified-out ${prefix}.unclassified.fastq" : "--unclassified-out ${prefix}.unclassified#.fastq"
     args += (reads.getName().endsWith(".gz") ? ' --gzip-compressed ' : '')
     """
     kraken2 \\
         --db $db \\
         --threads $task.cpus \\
-        --unclassified-out $unclassified \\
-        --classified-out $classified \\
+        $unclassified \\
+        $classified \\
         --report ${prefix}.kraken2.report.txt \\
         --output ${prefix}.kraken2.output.txt \\
         $paired \\