diff --git a/tests/software/bowtie/main.nf b/tests/software/bowtie/main.nf
index 1f6a54ff..8a64cd34 100644
--- a/tests/software/bowtie/main.nf
+++ b/tests/software/bowtie/main.nf
@@ -16,11 +16,10 @@ workflow test_bowtie_alignment_single_end {
 
     fasta = file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true)
     BOWTIE_INDEX ( fasta ) 
-}
 
     def input = []
     input = [ [ id:'test', single_end:true ], // meta map
               [ file("${launchDir}/tests/data/fastq/dna/Ecoli_DNA_R1.fastq.gz", checkIfExists: true) ] ]
-    BOWTIE_ALIGN ( input, BOWTIE_INDEX.index )
+    BOWTIE_ALIGN ( input, BOWTIE_INDEX.out.index )
 }
 
diff --git a/tests/software/bowtie/test.yml b/tests/software/bowtie/test.yml
index f1bd09fd..13b7b1fd 100644
--- a/tests/software/bowtie/test.yml
+++ b/tests/software/bowtie/test.yml
@@ -1,32 +1,42 @@
 - name: Run bowtie index
-  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_index -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_index -c tests/config/nextflow.config
   tags:
-    - bwa
-    - bwa_index
+    - bowtie
+    - bowtie_index
   files:
-    - path: output/bwa/NC_010473.fa.amb
-      md5sum: 942a990ae872f1c0b8d72dda2db405d5
-    - path: output/bwa/NC_010473.fa.bwt
-      md5sum: 7301b52e2ecb893d429a49fa692447ae
-    - path: output/bwa/NC_010473.fa.pac
-      md5sum: 4d5e6fc45bbc968f7f859e9ca2cc89ad
-    - path: output/bwa/NC_010473.fa.sa
-      md5sum: a47dcc92e750e2f16fbd979b8ff9538e
+    - path: output/bowtie/NC_010473.index.1.ebwt
+      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
+    - path: output/bowtie/NC_010473.index.2.ebwt
+      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
+    - path: output/bowtie/NC_010473.index.3.ebwt
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie/NC_010473.index.4.ebwt
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie/NC_010473.index.rev.1.ebwt
+      md5sum: 44f719c2fe42e1f35d54e798775846d1
+    - path: output/bowtie/NC_010473.index.rev.2.ebwt
+      md5sum: f3c398bba5158f4039334a932d79c051
 
-- name: Run bwa mem single-end
-  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_single_end -c tests/config/nextflow.config
+- name: Run bowtie index and align signle-end
+  command: nextflow run ./tests/software/bowtie -profile docker -entry test_bowtie_alignment_single_end -c tests/config/nextflow.config
   tags:
-    - bwa
-    - bwa_mem
+    - bowtie
+    - bwa_align
   files:
-    - path: output/test_single_end/test.bam
-      md5sum: 3ee21210bac387e0335008146e4728bc
+    - path: output/bowtie/NC_010473.index.1.ebwt
+      md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c
+    - path: output/bowtie/NC_010473.index.2.ebwt
+      md5sum: bfd10c5319c6a0dbc540fd789254a5dd
+    - path: output/bowtie/NC_010473.index.3.ebwt
+      md5sum: cd201e81724f3099131aec16ef2cc53b
+    - path: output/bowtie/NC_010473.index.4.ebwt
+      md5sum: bbb9d6d21ad765d135f95290204e8433
+    - path: output/bowtie/NC_010473.index.rev.1.ebwt
+      md5sum: 44f719c2fe42e1f35d54e798775846d1
+    - path: output/bowtie/NC_010473.index.rev.2.ebwt
+      md5sum: f3c398bba5158f4039334a932d79c051
+    - path: output/bowtie/test.out
+      md5sum: 6edce9d0d8ad7f5ce837a5be7e0d7fbe
+    - path: output/bowtie/test.sam
+      md5sum: acdb36ea915ac2ac71b69a0b704d9d8a
 
-- name: Run bwa mem paired-end
-  command: nextflow run ./tests/software/bwa -profile docker -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
-  tags:
-    - bwa
-    - bwa_mem
-  files:
-    - path: output/test_paired_end/test.bam
-      md5sum: 510d8acc6448c07cdacce8e64ec0904c