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pipeio_run: no wildcard filtering — need --filter-wildcards for single-session scoping

Summary

  • pipeio_run requires manually constructed absolute BIDS target paths. No way to scope a run to specific wildcards (e.g. subject/session).

Context

  • snakebids apps support --filter-{entity} {value} CLI flags for scoping runs
  • Currently the agent must inspect existing files to guess target paths, then pass full absolute paths
  • pipeio_target_paths (new tool) solves the path resolution side; this issue is about passing wildcard filters to the run itself

Possible fixes

  • [ ] Add wildcards: dict[str, str] param to pipeio_run that maps to --filter-{key} {value} flags
  • [ ] Alternatively, accept target expressions like {pipe}/{flow}:group/member[sub=01,ses=04] and resolve internally