`migrate`

Upgrade legacy G4X-output layouts

Brings older G4X outputs up to the latest schema used by G4X-viewer and G4X-helpers. The command renames or relocates legacy files, regenerates viewer artifacts when needed, and creates a backup before applying changes.

Usage

g4x-helpers migrate --help

Creates a backup in <G4X-DATA>/g4x_helpers/migration_backup before making any modifications.

Note

Global options --threads/-t & --verbose/-v must be supplied on the main entrypoint before the subcommand:

g4x-helpers --threads 16 -v 2 COMMAND /path/to/g4x_data [OPTIONS]

use g4x-helpers --help for more information

argument descriptions

required

`G4X-DATA` (argument)

Positional path to a G4X sample output directory.
The folder must follow the expected schema (e.g., run_meta.json, segmentation masks, panel files, single-cell outputs).
Provide this argument after command-specific options.

optional

`--restore`: (flag default: `False`)

Restore files from an existing migration backup (if present) instead of performing a migration. The backup directory is removed after a successful restore.

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