From 02ca314c89c786c4a94044f4dcdf3bdc2582d278 Mon Sep 17 00:00:00 2001
From: AymericGaudin <ay.gaudin@gmail.com>
Date: Wed, 3 Jun 2026 15:22:29 +0200
Subject: [PATCH 1/2] tools/scaling/scaling.py: Use one data folder for every
 workflow

---
 tools/scaling/scaling_cli.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tools/scaling/scaling_cli.py b/tools/scaling/scaling_cli.py
index 519288ab..023da373 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 = ""
@@ -632,7 +632,7 @@ 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(

From 72215a0a99fe35bb75a8ab63677b50a3afa4e21e Mon Sep 17 00:00:00 2001
From: AymericGaudin <ay.gaudin@gmail.com>
Date: Thu, 4 Jun 2026 10:53:06 +0200
Subject: [PATCH 2/2] tools/scaling/scaling.py: Change config.toml for group
 level (avoid data.tsv dependency)

---
 tools/scaling/scaling_cli.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tools/scaling/scaling_cli.py b/tools/scaling/scaling_cli.py
index 023da373..0665a257 100644
--- a/tools/scaling/scaling_cli.py
+++ b/tools/scaling/scaling_cli.py
@@ -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,