included test to ensure sex chr marker plots are created

lusSTR/tests/test_suite.py

@@ -289,11 +289,21 @@ def test_snakemake(command, output, format_out, convert_out, all_out, tmp_path):
     assert filecmp.cmp(exp_output, obs_output) is True
 
 
-def test_marker_plots(tmp_path):
+@pytest.mark.parametrize(
+    "sex",
+    [True, False],
+)
+def test_marker_plots(sex, tmp_path):
     inputfile = data_file("UAS_bulk_input/Positive Control Sample Details Report 2315.xlsx")
     exp_output = str(tmp_path / "MarkerPlots/lusstr_output_Positive_Control_marker_plots.pdf")
-    arglist = ["config", "-w", str(tmp_path), "--input", inputfile]
+    sex_exp = str(tmp_path / "MarkerPlots/lusstr_output_Positive_Control_sexchr_marker_plots.pdf")
+    if sex:
+        arglist = ["config", "-w", str(tmp_path), "--input", inputfile, "--sex"]
+    else:
+        arglist = ["config", "-w", str(tmp_path), "--input", inputfile]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
     snakemake_arglist = ["strs", "convert", "-w", str(tmp_path)]
     lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(snakemake_arglist))
     assert os.path.exists(exp_output) is True
+    if sex:
+        assert os.path.exists(sex_exp) is True