use _parent to name scratch subdirectories to match output directory base name

[rdmorin]

Because we are sharing scratch directories within larger projects, it would be convenient if the base directory for those defined by scratch_subdirectories was named the same as _parent. This would allow more than one pipeline running the same tool to avoid trying to write to the same subdirectory (i.e. it could be named uniquely via a distinct _parent in the config). It looks like the implementation would mirror what is currently being done in this if block.

# Configure output directory if not specified and create it
    if mconfig["dirs"].get("_parent") is None:
        root_output_dir = mconfig.get("root_output_dir", "results")
        output_dir = os.path.join(root_output_dir, f"{name}-{version}")
        mconfig["dirs"]["_parent"] = output_dir
    mconfig["dirs"]["_parent"] = mconfig["dirs"]["_parent"].rstrip("/") + "/"
    os.makedirs(mconfig["dirs"]["_parent"], exist_ok=True)

    # Update paths to conda environments to be relative to the module directory
    for env_name, env_val in mconfig["conda_envs"].items():
        if env_val is not None:
            mconfig["conda_envs"][env_name] = os.path.realpath(env_val)

Does anyone know of a reason we would not want to make this change?

Here's the current code that would need to be wrapped in a similar "if" block.

    # Setup output sub-directories
    scratch_subdirs = mconfig.get("scratch_subdirectories", [])
    mconfig = setup_subdirs(mconfig, subdirectories, scratch_subdirs)