diff --git a/tools/scaling/scaling_cli.py b/tools/scaling/scaling_cli.py index 95010885..134c52d9 100644 --- a/tools/scaling/scaling_cli.py +++ b/tools/scaling/scaling_cli.py @@ -517,7 +517,7 @@ def collect_config( print(f"- name: {workflow_name}") print(f"- type: {workflow_type}") print(f"- parameters: {workflow_parameters}") - output_dir = ( + config_dir = ( working_dir / f"{workflow_name}_{workflow_type}_{modality}" ) @@ -609,7 +609,7 @@ def collect_config( workflow_parameters = workflow_parameters.format_map( SafeDict({ "mod_names": ",".join(set(dfs.keys()) - {"mod"}), - "outdir": working_dir / "derivatives", + "outdir": working_dir, "fsdir": working_dir / "derivatives" / "sbm" }) ) @@ -618,15 +618,15 @@ def collect_config( confs = workflow_resource[workflow_name] selected_conf = confs.get(workflow_type, confs["default"]) - hopla_dir = output_dir / "hopla" - home_dir = output_dir / "home" + hopla_dir = config_dir / "hopla" + home_dir = config_dir / "home" for dir_ in (hopla_dir, home_dir): dir_.mkdir(parents=True, exist_ok=True) if infra == "slurm": image_parameters = ( f"--cleanenv --home {home_dir} --bind {bind_dir} " - f"--bind {output_dir} " + f"--bind {working_dir} " ) else: image_parameters = "" @@ -644,7 +644,7 @@ def collect_config( if df is not None: df.to_csv( - output_dir / "data.tsv", + config_dir / "data.tsv", sep="\t", index=False, ) @@ -670,7 +670,7 @@ def collect_config( hopla_dir=hopla_dir, ) config_path = ( - output_dir / + config_dir / f"config.toml" ) with config_path.open("w") as of: @@ -678,7 +678,7 @@ def collect_config( print(f"- configuration file: {config_path}") instructions_path = ( - output_dir / + config_dir / f"commands.txt" ) hopla_cmd = ( @@ -730,7 +730,7 @@ def scan_configs( Default None. with_hash : bool If True, compute a SHA-256 hash of each parsed file. - Dafault False. + Default False. with_longitudinal : bool If True, configure longitudinal workflows. Default True.