diff --git a/src/nf_modules/Kallisto/mapping_paired.nf b/src/nf_modules/Kallisto/mapping_paired.nf
index 15718373d0372803b78e316edec6f3e39343a0b1..4f4ad3d167292dcf9919506f89103dbbbab7f709 100644
--- a/src/nf_modules/Kallisto/mapping_paired.nf
+++ b/src/nf_modules/Kallisto/mapping_paired.nf
@@ -27,10 +27,10 @@ process mapping_fastq {
 
   script:
 """
-mkdir ${reads[0].baseName}
+mkdir ${pair_id}
 kallisto quant -i ${index} -t ${task.cpus} \
 --bias --bootstrap-samples 100 -o ${pair_id} \
-${reads[0]} ${reads[1]} &> ${pair_id}_kallisto_report.txt
+${reads[0]} ${reads[1]} &> ${pair_id}/kallisto_report.txt
 """
 }
 
diff --git a/src/nf_modules/Kallisto/mapping_single.nf b/src/nf_modules/Kallisto/mapping_single.nf
index cba5aff21d88cc43c142e6f075f8740d8a0506f8..97861e76faad7a266b279bb6fe8ac77964c94284 100644
--- a/src/nf_modules/Kallisto/mapping_single.nf
+++ b/src/nf_modules/Kallisto/mapping_single.nf
@@ -36,7 +36,7 @@ mkdir ${file_id}
 kallisto quant -i ${index} -t ${task.cpus} --single \
 --bias --bootstrap-samples 100 -o ${file_id} \
 -l ${params.mean} -s ${params.sd} \
-${reads} > ${file_id}_kallisto_report.txt
+${reads} &> ${file_id}/kallisto_report.txt
 """
 }