diff --git a/tests/data/profiles/expected-profile1.tsv b/tests/data/profiles/expected-profile1.tsv
new file mode 100644
index 0000000..9b938e1
--- /dev/null
+++ b/tests/data/profiles/expected-profile1.tsv
@@ -0,0 +1,4 @@
+sample_id	l1	l2	l3
+sample1	1	1	1
+sample2	1	1	1
+sample3	1	1	2
diff --git a/tests/pipelines/main.nf.test b/tests/pipelines/main.nf.test
index 0943982..ca901cf 100644
--- a/tests/pipelines/main.nf.test
+++ b/tests/pipelines/main.nf.test
@@ -16,7 +16,11 @@ nextflow_pipeline {
         then {
             assert workflow.success
             assert path("$launchDir/results").exists()
-            assert path("$launchDir/results/locidex/merged/profile.tsv").exists()
+
+            // Check MLST files
+            def actual_profile_tsv = path("$launchDir/results/locidex/merged/profile.tsv")
+            def expected_profile_tsv = path("$baseDir/tests/data/profiles/expected-profile1.tsv")
+            assert actual_profile_tsv.text == expected_profile_tsv.text
 
             // compare IRIDA Next JSON output
             def iridanext_json = path("$launchDir/results/iridanext.output.json").json