diff --git a/software/bwa/index/main.nf b/software/bwa/index/main.nf
index 47d2ec54..5613b86d 100644
--- a/software/bwa/index/main.nf
+++ b/software/bwa/index/main.nf
@@ -28,7 +28,8 @@ process BWA_INDEX {
     script:
     def software = getSoftwareName(task.process)
     """
-    bwa index $options.args $fasta
+    mkdir bwa
+    bwa index $options.args bwa/${fasta.baseName}
     echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
     """
 }