diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf
index 126c93ae..9fd19469 100644
--- a/modules/bowtie2/align/main.nf
+++ b/modules/bowtie2/align/main.nf
@@ -51,7 +51,7 @@ process BOWTIE2_ALIGN {
         $unaligned \\
         $args \\
         2> ${prefix}.bowtie2.log \\
-        | ${samtools}
+        | $samtools_command
 
     if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
         mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz