diff --git a/src/nf_modules/kallisto/main.nf b/src/nf_modules/kallisto/main.nf
index 67570e2d4739f025a646388407430cf7200dc705..b4d59dcae6c3be7054bad65b14176c49e4ae322d 100644
--- a/src/nf_modules/kallisto/main.nf
+++ b/src/nf_modules/kallisto/main.nf
@@ -40,7 +40,7 @@ process mapping_fastq {
   tuple val(file_id), path(reads)
 
   output:
-  tuple val(file_id), path("${pair_id}"), emit: counts
+  tuple val(file_id), path("${file_prefix}"), emit: counts
   tuple val(file_id), path("*_report.txt"), emit: report
 
   script: