Refactor container-related components of Boutiques descriptors

[michellewang]

• Right now the Boutiques descriptors cannot be run outside of Nipoppy because of the hardcoded [[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] in the "command-line" field.
• It would be better to change them to actual Boutiques inputs (e.g., [CONTAINER_COMMAND] and FPATH_CONTAINER, with defaults being [[NIPOPPY_CONTAINER_COMMAND]] and [[NIPOPPY_FPATH_CONTAINER]])
• This would not change the current behaviour at all, but would allow people to reuse the descriptors for other purposes (except that they might have to specify empty strings for the extra arguments)

[michellewang]

We also decided to no longer have Nipoppy-specific default values in the descriptor files themselves -- instead they will be stored in the default/sample invocation files

[michellewang]

It turns out that this is trickier than initially thought, because Boutiques will surround the container command with quotes (for security purposes). I have opened an issue for that, let's see if they respond.

Tentative descriptor modifications (for future reference):

{
    "command-line": "[CONTAINER_WRAPPER] dcm2bids [DICOM_DIR] [PARTICIPANT] [SESSION] [CONFIG] [OUTPUT_DIR] [AUTO_EXTRACT_ENTITIES] [BIDS_VALIDATE] [FORCE_DCM2BIDS] [SKIP_DCM2NIIX] [CLOBBER] [LOG_LEVEL] [VERSION]",
    "inputs": [
        {
            "id": "container_wrapper",
            "name": "container_wrapper",
            "description": "The full container command to run the tool, for example 'apptainer run container.sif'. By default this does not add anything to the command line",
            "optional": true,
            "type": "String",
            "value-key": "[CONTAINER_WRAPPER]",
            "default-value": null
        }
    ]
}

Corresponding invocation:

{
    "container_wrapper": "[[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]]",
    "dicom_dir": [
        "[[NIPOPPY_DPATH_SOURCEDATA]]/[[NIPOPPY_PARTICIPANT]]/[[NIPOPPY_SESSION]]"
    ],
    "participant": "[[NIPOPPY_PARTICIPANT]]",
    "session": "[[NIPOPPY_SESSION_SHORT]]",
    "config": "[[DCM2BIDS_CONFIG_FILE]]",
    "output_dir": "[[NIPOPPY_DPATH_BIDS]]"
}

Doesn't work because whatever is in "container_wrapper" gets surrounded by single quotes :/

[michellewang]

After chatting with Mathieu at OHBM brainhack, we found a workaround using environment variables (e.g. replace [[NIPOPPY_CONTAINER_COMMAND]] with $NIPOPPY_CONTAINER_COMMAND and setting the environment variables before running bosh