Add breaking test for cutadapt without opts

tests/unit/rules/test_adapter_removal_paired.py

@@ -111,3 +111,51 @@ def test_adapater_removal_paired_no_adapters(setup):
     assert os.path.islink(lr2)
     assert os.path.islink(sr1)
     assert os.path.islink(sr2)
+
+
+def test_adapater_removal_paired_no_opts(setup):
+    output_dir = setup
+    sunbeam_output_dir = output_dir / "sunbeam_output"
+    lr1 = sunbeam_output_dir / "qc" / "01_cutadapt" / "SHORT_1.fastq.gz"
+    lr2 = sunbeam_output_dir / "qc" / "01_cutadapt" / "SHORT_2.fastq.gz"
+    sr1 = sunbeam_output_dir / "qc" / "01_cutadapt" / "LONG_1.fastq.gz"
+    sr2 = sunbeam_output_dir / "qc" / "01_cutadapt" / "LONG_2.fastq.gz"
+
+    config_str = f"qc: {{cutadapt_opts: ''}}"
+    sp.check_output(
+        [
+            "sunbeam",
+            "config",
+            "modify",
+            "-i",
+            "-s",
+            config_str,
+            f"{output_dir / 'sunbeam_config.yml'}",
+        ]
+    )
+
+    sp.check_output(
+        [
+            "sunbeam",
+            "run",
+            "--profile",
+            f"{output_dir}",
+            "--notemp",
+            "--allowed-rules=adapter_removal_paired",
+            "--rerun-triggers=input",
+            f"{lr1}",
+            f"{lr2}",
+            f"{sr1}",
+            f"{sr2}",
+        ]
+    )
+
+    assert lr1.stat().st_size >= 50000
+    assert lr2.stat().st_size >= 50000
+    assert sr1.stat().st_size >= 10000
+    assert sr2.stat().st_size >= 10000
+
+    with gzip.open(lr1) as f1, gzip.open(lr2) as f2:
+        assert len(f1.readlines()) == len(f2.readlines())
+    with gzip.open(sr1) as f1, gzip.open(sr2) as f2:
+        assert len(f1.readlines()) == len(f2.readlines())

workflow/envs/reports.linux-64.pin.txt

@@ -5,37 +5,37 @@
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