diff --git a/src/nf_modules/bwa/main.nf b/src/nf_modules/bwa/main.nf
index 39ee81575b6f2c2f9683606b2794a299f88e3b5d..1e4da4bd0cff66a2af2c56de58bd2b49338ee02a 100644
--- a/src/nf_modules/bwa/main.nf
+++ b/src/nf_modules/bwa/main.nf
@@ -66,7 +66,7 @@ bwa_mem_R = "@RG\\tID:${library}\\tSM:${library}\\tLB:lib_${library}\\tPL:illumi
 bwa mem -t ${task.cpus} \
 ${params.mapping_fastq} \
 -R '${bwa_mem_R}' \
-${index.baseName} ${reads[0]} ${reads[1]} 2> \
+${index[0].baseName} ${reads[0]} ${reads[1]} 2> \
   ${file_prefix}_bwa_report.txt | \
   samtools view -@ ${task.cpus} -Sb - > ${file_prefix}.bam
 """
@@ -75,7 +75,7 @@ ${index.baseName} ${reads[0]} ${reads[1]} 2> \
 bwa mem -t ${task.cpus} \
 ${params.mapping_fastq} \
 -R '${bwa_mem_R}' \
-${index.baseName} ${reads} 2> \
+${index[0].baseName} ${reads} 2> \
   ${file_prefix}_bwa_report.txt | \
   samtools view -@ ${task.cpus} -Sb - > ${file_prefix}.bam
 """