pipeio_run wildcards parameter doesn't filter snakebids sessions¶
Observed: pipeio_run(flow="preprocess_motion", wildcards={"subject": "02", "session": "03"}) passes wildcards as --config subject=02 --config session=03 but this doesn't filter snakebids generate_inputs(). All 48 sessions were included in the DAG and executed.
Workaround: Used explicit absolute target paths via pipeio_target_paths to scope the run.
Expected: Wildcard filtering should actually limit which sessions are processed, either by passing --config pybids_inputs.motion.filters.subject=02 or by pre-filtering the target list.
Source context: pixecog¶
PixEcog (pixecog): Neuropixels and ECoG dataset and analysis
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Related Notes¶
- issue-arash-20260409-232128-727233.md — Directly related: both concern pipeio_run failing to correctly pass filter/wildcard parameters to snakemake — same root cause area
- issue-arash-20260409-232102-577698.md — Same pipeio_run tool; adjacent runtime failure that may share underlying parameter-handling bugs