diff --git a/snappy_pipeline/workflows/ngs_mapping/__init__.py b/snappy_pipeline/workflows/ngs_mapping/__init__.py index 1b0c5baa2..bae2055d3 100644 --- a/snappy_pipeline/workflows/ngs_mapping/__init__.py +++ b/snappy_pipeline/workflows/ngs_mapping/__init__.py @@ -926,10 +926,15 @@ def get_output_files(self, action): paths_work = getattr(self, f"_get_output_files_{action}_work")() yield from paths_work.items() # Return list of paths to the links that will be created in ``output/`` - yield "output_links", [ - re.sub(r"^work/", "output/", work_path) - for work_path in chain(paths_work.values(), self.get_log_file(action).values()) - ] + paths_all = list(paths_work.values()) + paths_logs = self.get_log_file(action) + if isinstance(paths_logs, dict): + paths_all += list(paths_logs.values()) + elif isinstance(paths_logs, list): + paths_all += paths_logs + elif isinstance(paths_logs, str): + paths_all.append(paths_logs) + yield "output_links", [re.sub(r"^work/", "output/", work_path) for work_path in paths_all] @dictify def _get_output_files_run_work(self):