diff --git a/CHANGELOG.md b/CHANGELOG.md
index 130819513..dfeded678 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -93,6 +93,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1324](https://github.com/nf-core/rnaseq/pull/1324) - Fix tags entries and rename pipeline level tests
 - [PR #1325](https://github.com/nf-core/rnaseq/pull/1325) - Minor fixes to strandedness settings and messaging
 - [PR #1326](https://github.com/nf-core/rnaseq/pull/1326) - Move Conda dependencies for local modules to individual environment file
+- [PR #1328](https://github.com/nf-core/rnaseq/pull/1328) - Add pipeline level test for STAR-RSEM and HISAT2
 - [PR #1329](https://github.com/nf-core/rnaseq/pull/1329) - Remove tags from all nf-test files
 
 ### Parameters
diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test
new file mode 100644
index 000000000..c8b55906e
--- /dev/null
+++ b/tests/hisat2.nf.test
@@ -0,0 +1,20 @@
+nextflow_pipeline {
+
+    name "Test pipeline with HISAT2 aligner"
+    script "../main.nf"
+
+    test("Params: --aligner hisat2") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = 'hisat2'
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+    }
+}
+
diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test
new file mode 100644
index 000000000..3a0b867a9
--- /dev/null
+++ b/tests/star_rsem.nf.test
@@ -0,0 +1,20 @@
+nextflow_pipeline {
+
+    name "Test pipeline with STAR aligner and RSEM for quantification"
+    script "../main.nf"
+
+    test("Params: --aligner star_rsem") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                aligner = 'star_rsem'
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+    }
+}
+