Improve warning messages

crocodeel/crocodeel.py

@@ -249,13 +249,6 @@ def main() -> None:
         ContaminationEventIO.write_tsv(conta_events, args.conta_events_fh)
         args.conta_events_fh.close()
 
-        if args.command != "test_install":
-            logging.warning("Contamination events may be false positives, especially "
-                            "when dealing with samples with similar species abundance profiles "
-                            "(longitudinal data, animals raised together)")
-            logging.warning("Check each reported contamination event by inspecting "
-                            "scatterplots generated by the plot_conta subcommand")
-
     # Or load them
     if args.command == "plot_conta":
         conta_events = ContaminationEventIO.read_tsv(args.conta_events_fh)
@@ -274,6 +267,17 @@ def main() -> None:
             args.color_conta_species,
         )
 
+    if args.command in ("easy_wf", "search_conta") and conta_events:
+        logging.warning("Contamination events may be false positives, especially "
+                            "when dealing with samples with similar species abundance profiles "
+                            "(longitudinal data, animals raised together)")
+        if args.command == "search_conta":
+            logging.warning("Check each reported contamination event by inspecting "
+                            "scatterplots generated by the plot_conta subcommand")
+        else:
+            logging.warning("Check each reported contamination event by inspecting "
+                "scatterplots in the PDF report %s", Path(args.pdf_report_fh.name).resolve())
+
     if args.command == "test_install":
         if filecmp.cmp(TestData.EXPECTED_CONTA_EVENTS_FILE, args.conta_events_fh.name):
             logging.info(