diff --git a/tests/pipeline/bismark/assets/samplesheet.csv b/tests/pipeline/bismark/assets/samplesheet.csv
new file mode 100644
index 00000000..d51cf60f
--- /dev/null
+++ b/tests/pipeline/bismark/assets/samplesheet.csv
@@ -0,0 +1,10 @@
+sample,fastq_1,fastq_2,genome
+SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,
+SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,
+SRR389222_merge,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,
+SRR389222_merge,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,
+SRR389222_merge,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,,
+Ecoli_uniq1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,
+Ecoli_uniq2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,
+Ecoli_merge,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,
+Ecoli_merge,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,
diff --git a/tests/pipeline/bismark/samplesheet.nf.test b/tests/pipeline/bismark/samplesheet.nf.test
new file mode 100644
index 00000000..ca5e29fe
--- /dev/null
+++ b/tests/pipeline/bismark/samplesheet.nf.test
@@ -0,0 +1,24 @@
+nextflow_pipeline {
+
+    name "Test Replicate Handling"
+    script "main.nf"
+
+    tag "pipeline"
+
+    test("Should handle replicates and works") {
+        when {
+            params {
+                aligner        = "bismark"
+                save_reference = true
+                input          = "$baseDir/tests/pipeline/bismark/assets/samplesheet.csv"
+                outdir         = "$outputDir"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success }
+            )
+        }
+    }
+}
diff --git a/tests/pipeline/bismark/samplesheet.nf.test.snap b/tests/pipeline/bismark/samplesheet.nf.test.snap
new file mode 100644
index 00000000..916a0ad8
--- /dev/null
+++ b/tests/pipeline/bismark/samplesheet.nf.test.snap
@@ -0,0 +1,12 @@
+{
+    "single_end_software_versions": {
+        "content": [
+            "{BISMARK_ALIGN={bismark=0.24.0}, BISMARK_GENOMEPREPARATION={bismark=0.24.0}, FASTQC={fastqc=0.12.1}, QUALIMAP_BAMQC={qualimap=2.2.2-dev}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, Workflow={nf-core/methylseq=v2.7.0dev}}"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.0"
+        },
+        "timestamp": "2024-05-17T14:37:44.368983"
+    }
+}
\ No newline at end of file