diff --git a/src/nf_modules/Bowtie/bowtie.nf b/src/nf_modules/Bowtie/bowtie.nf
index 21e329596d659ff46398bd3a5ab21556351c357c..54d10daf5f44dbc6eac3fe337dddffe93b81c597 100644
--- a/src/nf_modules/Bowtie/bowtie.nf
+++ b/src/nf_modules/Bowtie/bowtie.nf
@@ -25,6 +25,7 @@ process index_fasta {
 
   output:
     file "*.index*" into index_files
+    file "*_report.txt" into indexing_report
 
   script:
 """
@@ -68,6 +69,7 @@ process mapping_fastq {
 
   output:
   file "*.bam" into bam_files
+  file "*_report.txt" into mapping_report
 
   script:
   index_id = index[0]
@@ -119,6 +121,7 @@ process mapping_fastq {
 
   output:
   file "*.bam" into bam_files
+  file "*_report.txt" into mapping_report
 
   script:
 index_id = index[0]
diff --git a/src/nf_modules/Bowtie/tests/index.nf b/src/nf_modules/Bowtie/tests/index.nf
index 0b3ca58b227f49f3af6a69299ed882806f5e5cba..f9ee2ebae6d12a0b5233cdd7dbcdf25ae438e315 100644
--- a/src/nf_modules/Bowtie/tests/index.nf
+++ b/src/nf_modules/Bowtie/tests/index.nf
@@ -17,6 +17,7 @@ process index_fasta {
 
   output:
     file "*.index*" into index_files
+    file "*_report.txt" into indexing_report
 
   script:
 """
diff --git a/src/nf_modules/Bowtie/tests/mapping_paired.nf b/src/nf_modules/Bowtie/tests/mapping_paired.nf
index fdf9aee42a5a20e3cc86d864ac06ea581073ed1b..6ea2d70ad18ec6273fe87e8d8f7d34f41f2b82ac 100644
--- a/src/nf_modules/Bowtie/tests/mapping_paired.nf
+++ b/src/nf_modules/Bowtie/tests/mapping_paired.nf
@@ -24,11 +24,12 @@ process mapping_fastq {
 
   output:
   file "*.bam" into bam_files
+  file "*_report.txt" into mapping_report
 
   script:
   index_id = index[0]
   for (index_file in index) {
-    if (index_file =~ /.*\.1\.ebwt/) {
+  if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
         index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
     }
   }
diff --git a/src/nf_modules/Bowtie/tests/mapping_single.nf b/src/nf_modules/Bowtie/tests/mapping_single.nf
index e8781267fd3f75b579ab9111d13a07779927c2a4..551b90cedcfc4dfbf13fb619b83b01b3006b1067 100644
--- a/src/nf_modules/Bowtie/tests/mapping_single.nf
+++ b/src/nf_modules/Bowtie/tests/mapping_single.nf
@@ -23,17 +23,18 @@ process mapping_fastq {
 
   output:
   file "*.bam" into bam_files
+  file "*_report.txt" into mapping_report
 
   script:
 index_id = index[0]
 for (index_file in index) {
-  if (index_file =~ /.*\.1\.ebwt/) {
+  if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
       index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
   }
 }
 """
 bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
--U ${reads} 2> \
+-q ${reads} 2> \
 ${reads.baseName}_bowtie_report.txt | \
 samtools view -Sb - > ${reads.baseName}.bam
 
diff --git a/src/nf_modules/Bowtie2/bowtie2.nf b/src/nf_modules/Bowtie2/bowtie2.nf
index 8ec01cc7331ae738136f9f65b63fa0aeda6f14e4..3a51b5c441cd3fab8e4d6011d3bf84c442a51fa9 100644
--- a/src/nf_modules/Bowtie2/bowtie2.nf
+++ b/src/nf_modules/Bowtie2/bowtie2.nf
@@ -25,6 +25,7 @@ process index_fasta {
 
   output:
     file "*.index*" into index_files
+    file "*_report.txt" into indexing_report
 
   script:
 """
diff --git a/src/nf_modules/Bowtie2/tests/index.nf b/src/nf_modules/Bowtie2/tests/index.nf
index 2636f4be09ab1ff24142ab64ba9bf932f44a2233..4f3cde5e990f3528f2f000c8e68131edafdecf97 100644
--- a/src/nf_modules/Bowtie2/tests/index.nf
+++ b/src/nf_modules/Bowtie2/tests/index.nf
@@ -17,6 +17,7 @@ process index_fasta {
 
   output:
     file "*.index*" into index_files
+    file "*_report.txt" into indexing_report
 
   script:
 """