diff --git a/src/nf_modules/Bowtie2/bowtie2.nf b/src/nf_modules/Bowtie2/bowtie2.nf
index 18c1479be848a7ebef5ef1de709d6de19f23fe4e..8ec01cc7331ae738136f9f65b63fa0aeda6f14e4 100644
--- a/src/nf_modules/Bowtie2/bowtie2.nf
+++ b/src/nf_modules/Bowtie2/bowtie2.nf
@@ -72,7 +72,7 @@ process mapping_fastq {
   script:
   index_id = index[0]
   for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
         index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
     }
   }
@@ -122,7 +122,7 @@ process mapping_fastq {
   script:
   index_id = index[0]
   for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
         index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
     }
   }
diff --git a/src/nf_modules/Bowtie2/tests/mapping_paired.nf b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
index d102ebb390aad690dbd076d89574697d088bc860..4cacca43e6a9dc45fbd9c4dde329d2499289f72d 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_paired.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_paired.nf
@@ -29,7 +29,7 @@ process mapping_fastq {
   script:
   index_id = index[0]
   for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
         index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
     }
   }
diff --git a/src/nf_modules/Bowtie2/tests/mapping_single.nf b/src/nf_modules/Bowtie2/tests/mapping_single.nf
index 568a68ea1983a13336da7653113a0de047bc2859..19f491af7dab4092f8e9997561b0c4f8824d7293 100644
--- a/src/nf_modules/Bowtie2/tests/mapping_single.nf
+++ b/src/nf_modules/Bowtie2/tests/mapping_single.nf
@@ -28,7 +28,7 @@ process mapping_fastq {
   script:
   index_id = index[0]
   for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
         index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
     }
   }