diff --git a/tools/scaling/scaling_cli.py b/tools/scaling/scaling_cli.py index 519288ab..0665a257 100644 --- a/tools/scaling/scaling_cli.py +++ b/tools/scaling/scaling_cli.py @@ -310,7 +310,7 @@ def organize_longitudinal( """ banner = r""" +----------------------------------+ - | Organize longitudianl data... | + | Organize longitudinal data... | +----------------------------------+ """ print(banner) @@ -482,7 +482,7 @@ def collect_config( else None ) workflow_parameters = workflow_parameters.format_map( - SafeDict({"outdir": output_dir / "data"}) + SafeDict({"outdir": working_dir / "data"}) ) print(f"- edited parameters: {workflow_parameters}") @@ -497,7 +497,7 @@ def collect_config( if infra == "slurm": image_parameters = ( f"--cleanenv --home {home_dir} --bind {bind_dir} " - f"--bind {output_dir} " + f"--bind {working_dir} " ) else: image_parameters = "" @@ -520,12 +520,16 @@ def collect_config( index=False, ) + commands = f'"brainprep {workflow_id} {workflow_parameters}"' + if "group" in workflow_id: + commands = f"[[{commands}]]" + config_template = config_file.read_text() config_str = config_template.format( name=workflow_name, operator="TO UPDATE", date=str(datetime.now().date()), - commands=f'"brainprep {workflow_id} {workflow_parameters}"', + commands=commands, parameters=image_parameters, cluster=infra, partition=partition, @@ -632,7 +636,7 @@ def scan_configs( print("No cache files found. Parsing data.") selected = None else: - print("Multiple cache files found:") + print("Cache file(s) found:") for idx, path in enumerate(cache_files, 1): print(f"{idx}. {path.name}") choice = input(