diff --git a/src/sophios/compiler.py b/src/sophios/compiler.py index 90f81ce8..f3abb0fb 100644 --- a/src/sophios/compiler.py +++ b/src/sophios/compiler.py @@ -319,7 +319,7 @@ def compile_workflow_once(yaml_tree_ast: YamlTree, # Use auto-discovery mechanism (with run tag) tool_i = tools[stepid_runtag] else: - msg = f'Error! Neither {stepid.stem} nor {stepid_runtag.stem} found!' + msg = f"Error! Neither {stepid.stem} nor {stepid_runtag.stem} found!, check your 'search_paths_cwl' in global_config.json" raise Exception(msg) # Programmatically modify tool_i here graph_dummy = graph # Just use anything here to satisfy mypy diff --git a/src/sophios/input_output.py b/src/sophios/input_output.py index 6bf5c809..7c486051 100644 --- a/src/sophios/input_output.py +++ b/src/sophios/input_output.py @@ -138,7 +138,7 @@ def write_config_to_disk(config: Json, config_file: Path) -> None: # make the full path if it doesn't exist config_dir.mkdir(parents=True, exist_ok=True) with open(config_file, 'w', encoding='utf-8') as f: - json.dump(config, f) + json.dump(config, f, indent=4, sort_keys=True) def get_config(config_file: Path, default_config_file: Path) -> Json: