diff --git a/workflows/tests/bugs/replicates_same_filename/main.nf.test b/workflows/tests/bugs/replicates_same_filename/main.nf.test
new file mode 100644
index 00000000..0664c3a6
--- /dev/null
+++ b/workflows/tests/bugs/replicates_same_filename/main.nf.test
@@ -0,0 +1,45 @@
+nextflow_pipeline {
+
+    name "Replicates"
+    script "../../../../main.nf"
+    tag "bug"
+
+    // BUG https://github.com/nf-core/nascent/issues/159
+    test("Should fail with replicates that have the same filename") {
+        when {
+            params {
+                outdir = "$outputDir"
+                input = "${projectDir}/workflows/tests/bugs/replicates_same_filename/replicates_same_filename.csv"
+            }
+        }
+
+        then {
+            // FIXME this fails at FASTQC but should fail at nf-validation
+            // Might get fixed in nf-schema?
+            assert workflow.failed
+            assert snapshot(
+                workflow.trace.tasks().size(),
+            ).match()
+        }
+    }
+
+    // BUG https://github.com/nf-core/nascent/issues/159
+    test("Should work with replicates that have the same id and different file names") {
+        when {
+            params {
+                outdir = "$outputDir"
+                input = "${projectDir}/workflows/tests/bugs/replicates_same_filename/same_id.csv"
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.trace.tasks().size(),
+                ).match()
+                }
+            )
+        }
+    }
+}
diff --git a/workflows/tests/bugs/replicates_same_filename/main.nf.test.snap b/workflows/tests/bugs/replicates_same_filename/main.nf.test.snap
new file mode 100644
index 00000000..ff74c64f
--- /dev/null
+++ b/workflows/tests/bugs/replicates_same_filename/main.nf.test.snap
@@ -0,0 +1,18 @@
+{
+    "Should fail with replicates that have the same filename": {
+        "content": [0],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T12:24:05.004711151"
+    },
+    "Should work with replicates that have the same id and different file names": {
+        "content": [31],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T14:52:05.603228732"
+    }
+}
diff --git a/workflows/tests/bugs/replicates_same_filename/replicates_same_filename.csv b/workflows/tests/bugs/replicates_same_filename/replicates_same_filename.csv
new file mode 100644
index 00000000..ab3ae47e
--- /dev/null
+++ b/workflows/tests/bugs/replicates_same_filename/replicates_same_filename.csv
@@ -0,0 +1,3 @@
+sample,fastq_1,fastq_2
+SAMPLE_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882903_T3.fastq.gz,
+SAMPLE_REP1,https://github.com/nf-core/test-datasets/raw/nascent/testdata/SRX882903_T3.fastq.gz,
diff --git a/workflows/tests/bugs/replicates_same_filename/same_id.csv b/workflows/tests/bugs/replicates_same_filename/same_id.csv
new file mode 100644
index 00000000..bc7eaecf
--- /dev/null
+++ b/workflows/tests/bugs/replicates_same_filename/same_id.csv
@@ -0,0 +1,3 @@
+sample,fastq_1,fastq_2
+SAMPLE_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882903_T1.fastq.gz,
+SAMPLE_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882903_T2.fastq.gz,