diff --git a/modules/minimap2/align/main.nf b/modules/minimap2/align/main.nf
index 7ba05ee9..08ac6eef 100644
--- a/modules/minimap2/align/main.nf
+++ b/modules/minimap2/align/main.nf
@@ -27,8 +27,8 @@ process MINIMAP2_ALIGN {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
     def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
-    def cigar_paf = cigar_paf_format && !sam_format ? "-c" : ''
-    def set_cigar_bam = cigar_bam && sam_format ? "-L" : ''
+    def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
+    def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
     """
     minimap2 \\
         $args \\