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Standardize arguments w.r.t. other BIDS Apps #218

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tsalo opened this issue Mar 19, 2025 · 2 comments
Open

Standardize arguments w.r.t. other BIDS Apps #218

tsalo opened this issue Mar 19, 2025 · 2 comments
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breaking-change PRs that change results or interfaces. enhancement New feature or request

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@tsalo
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tsalo commented Mar 19, 2025

Summary

Many of the BABS parameters, such as --where_project, are kind of clunky and nonstandard across other packages, like datalad or BIDS Apps.

@tsalo tsalo added enhancement New feature or request breaking-change PRs that change results or interfaces. labels Mar 19, 2025
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tsalo commented Mar 19, 2025

  • --input (babs init) --> --datasets, based on XCP-D, QSIPrep, etc. We can also change the pattern from <name> <path> to <name>=<path> to match how those BIDS Apps work.
  • --list_sub_file (babs init) --> I'm not sure what the name should be, but it seems like we should be accepting a participants TSV file with participant_id and session_id instead of a CSV with sub_id and ses_id.
  • --container_ds and --container_name (babs init) --> --container. We have --input set up as pairs of names and paths, so it seems weird to not do that with the containers too. I'd have it as --container <name>=<path>.
  • --container_config_yaml_file (babs init, babs-status) --> --config.
  • --type_session (babs init) --> --dataset-type
  • --type_system (babs init) --> --queue to match Heudiconv
  • --job_account (babs status) --> I don't know, but this one's confusingly named.

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tsalo commented Mar 20, 2025

Per @mattcieslak instead of --config, do --container-config.

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