mdiazmel
commented
2 years ago If we remain attached to the original Clinica's philosophy (i.e. try to make the CLI as simple as possible), the option of implicit passing seems to be the most adequate choice (at least for the default behavior) . We must, of course, provide the necessary tools/instructions to download the resources (and where to store them) if remote fetching fails. It's also possible to think about providing "an expert mode", for users who want to pass explicitly the resources to the pipeline.
github-actions[bot]
Some pipelines require additional resources (such as atlasses or mappings) which we do not want to bundle within Clinica for various reasons like size or licensing terms. Nonetheless, Clinica may download those at runtime and feed them to the pipelines.
However, Clinica may be deployed in an execution environment where remote fetching is not possible, like a cluster. In this case, Clinica needs access to these files either by explicit or implicit parameter passing. With explicit passing, the pipeline would provide CLI options for each file which then overrides the remote fetching mechanism. With implicit passing, Clinica would look up for files within a user-readable resource directory and fallback to remote fetching, or the other way around.
Both have their pros and cons to be discussed.